Methods and compositions for regulating gene expression in plant cells

ABSTRACT

Novel chimeric plant promoter sequences are provided, together with plant gene expression cassettes comprising such sequences. Novel transcription factors are provided, together with nucleic acid sequences encoding such transcription factors and plant gene expression cassettes comprising such nucleic acid sequences. Methods for using the chimeric plant promoter sequences and novel transcription factors in regulating the expression of at least one gene of interest are provided, together with transgenic plants comprising such chimeric plant promoter sequences and novel transcription factors.

FIELD OF THE INVENTION

The present invention relates to the field of molecular biology. Inparticular, the invention relates to methods and compositions that canbe used to regulate gene expression. Still more particularly, theinvention relates to methods and compositions that can be used toinitiate and/or enhance the expression of at least one gene of interestin plant cells.

BACKGROUND OF THE INVENTION

Gene expression may be regulated in several ways, which include theactivation or suppression of transcription, the differential processingand stabilization of messenger RNA (“mRNA”) and the extent oftranslation of the mRNA. The control of transcription plays aparticularly critical role in the regulation of gene expression ineukaryotic cells. There are several structural elements that areinvolved in the regulation of transcription.

Promoters represent a class of nucleic acid structures that are involvedin the regulation of transcription. In general, promoters are locatednext to the transcription start site and interact with RNA polymerase,either directly or indirectly. Promoters often comprise several discrete“cis elements,” each of which may be recognized by one or moretrans-acting regulatory proteins known as transcription factors. Amongthe various cis elements well-known in the art is the “TATA box,” whichis known to interact with certain regulatory proteins, e.g.,transcription factors, and is generally located about 20-30 base pairsupstream from the transcription initiation site.

The binding of such transcription factors to promoters or otherregulatory sequences is often responsible for the initiation,maintenance and/or down-regulation of transcription. A typicalgene-specific eukaryotic transcription factor includes a DNA-bindingdomain and one or more additional domains that influence the activationor repression of transcription, e.g., “trans-acting domains.”Transcription factors bind in the general proximity (althoughoccasionally at great distances) of the point of transcriptioninitiation of a gene. Such transcription factors often act to influencethe efficiency of formation or function of a transcription initiationcomplex at the promoter. Transcription factors can act in a positivefashion (transactivation) or in a negative fashion (transrepression).Furthermore, the effect that transcription factors may have on geneexpression can be constitutive (always “on”) or conditional.

Over the years, several classes of DNA-binding domains of varioustranscription factors have been characterized and the nucleic acidsequences to which such domains interact identified. Non-limitingexamples of such domains include motifs known as the leucine zipper, thebZIP domain, the zinc-finger, the homeobox, the basic helix-loop-helixand others. The trans-acting domains of transcription factors are oftencharacterized as having a high content of specific amino acids, whichinclude domains rich in acidic amino acids, proline or glutamine(Giniger et al., 1985; Meshi and Iwabuchi, 1995; Mitchell and Tjian,1989). Acidic domains have been reported to possess activation functionsthat include interactions with TATA-binding proteins (“TBP”) (Truant etal., 1993), TBP-associated factors (“TAFs”) (Uesugi et al., 1997), TFIIA(Pugh, 2000), TFIIB (Klemm et al., 1995) and other general transcriptioncomplexes (Stargell and Struhl, 1995).

Beachy, in U.S. Pat. No. 5,824,857 entitled “Plant Promoter,” describedthe promoter from the rice tungro bacilliform virus (“RTBV”). The '857patent discloses that the RTBV promoter causes preferential geneexpression in plant vascular tissue. The patent also discloses that theRTBV promoter can be used to drive expression in most plants, whethermonocotyledonous or dicotyledonous, and is particularly suited to rice.The patent further discloses the transformation of plants by insertingthe coding sequence of the RTBV promoter and a heterologous gene ofinterest to obtain transgenic plants that express the gene of interestin vascular tissue.

Yin and Beachy, in “The regulatory regions of the rice tungrobacilliform virus promoter and interacting nuclear factors in rice(Oryza sativa L.), The Plant Journal, 7(6): 969-980 (1995),” describedthe E fragment (−164 to +45 in relation to the transcription start site)within the RTBV promoter, which was shown to be sufficient to causetissue-specific gene expression. The article also disclosed a criticalcis element, Box II (−53 to −39), within the E fragment that was shownto be essential for promoter activity. The same authors identified othercis elements of the RTBV promoter in “Promoter elements required forphloem-specific gene expression from the RTBV promoter in rice, ThePlant Journal: 12(5): 1179-1188 (1997),” including the ASL Box (−98 to−79) and a GATA motif (−143 to −135). Together, these cis elements wereshown to confer phloem-specific reporter gene expression.

Yin et al., in “RF2a, a bZIP transcriptional activator ofphloem-specific rice tungro bacilliform virus promoter, function invascular development, The EMBO Journal, 16(17): 5247-5259 (1997),”identified a 1.8 Kb transcription factor consisting of 368 aminoacids—designated as RF2a. The RF2a transcription factor is currentlyknown to represent a bZIP transcription activator found in rice plantsthat contains acidic, proline-rich and glutamine-rich putativefunctional domains. RF2a has been shown to bind the Box II element ofthe RTBV promoter and stimulate Box II-dependent transcription in vitro.Another bZIP protein, RF2b, has been isolated through interaction withRF2a, which also has been shown to interact with the Box II element.

The inventors have discovered that the Box II cis-element of the RTBVpromoter is portable and that it can be used to modulate gene expressionin unrelated promoters in connection with RF2a and/or RF2b. That is,until now, it was not known that the Box II element, and similarsequences, could be used in chimeric promoters to regulate geneexpression in connection with RF2a and/or RF2b. What's more, theinventors have discovered that the acidic domain of RF2a is particularlycritical to the activation function of this transcription factor andthat it can be transferred to unrelated DNA-binding proteins to modulategene expression. Accordingly, the inventors have discovered a new systemfor modulating gene expression, which, preferably, involves the Box IIcis-element, operational derivatives of the Box II element, RF2a, RF2b,and/or DNA-binding proteins that comprise amino acid sequences that areat least substantially similar to the acidic domain of RF2a.

SUMMARY OF THE INVENTION

Until now, it was not known that the Box II element of the RTBV promoteris portable and that it can be used in connection with unrelatedpromoters to activate and/or enhance gene expression in the presence ofRF2a and/or RF2b. Similarly, the inventors have discovered thatoperational derivatives of the Box II element can be used to regulategene expression in like fashion. Still further, the inventors havediscovered that the acidic domain of RF2a is also portable and that itcan be transferred to unrelated DNA-binding proteins to activate and/orenhance gene expression.

Accordingly, the present invention exploits the portability of the BoxII sequence, its operational derivatives and its interaction with RF2aand/or RF2b to provide novel compositions and methods that can be usedto control the expression of one or more genes of interest. Further, thepresent invention provides novel transcription factors, which contain atleast one domain that comprises an amino acid sequence that is at leastsubstantially similar to the acidic domain of RF2a, which can be used inconnection with unrelated DNA-binding domains to regulate geneexpression.

In one preferred embodiment, the invention provides novel chimericpromoters, which comprise (a) nucleic acid sequences derived from anypromoter (other than the RTBV promoter), or promoter fragment, that arecapable of driving gene expression in plant cells and (b) at least onenucleic acid sequence selected from the group consisting of: (i) SEQ IDNO:1; (ii) SEQ ID NO:2; (iii) SEQ ID NO:3; and (iv) sequences that aresubstantially similar to either SEQ ID NO:1, 2, or 3. The nucleic acidsequence consisting of SEQ ID NO:1, 2, 3 or sequences substantiallysimilar to any of the foregoing sequences, is, preferably, located in aposition that is approximately 7 nucleotides from the TATA box of thepromoter, or promoter fragment, plus one or more full turns of DNAhelix.

In another preferred embodiment, the invention provides plant geneexpression cassettes that comprise a first chimeric promoter, whichcomprises a nucleic acid sequence selected from the group consisting of:(i) SEQ ID NO:1; (ii) SEQ ID NO:2; (iii) SEQ ID NO:3; and (iv) sequencesthat are substantially similar to either SEQ ID NO:1, 2, or 3. The firstchimeric promoter is operatively linked to any gene of interest. Thenucleic acid sequence consisting of SEQ ID NO:1, 2, 3 or sequencessubstantially similar to any of the foregoing sequences, is, preferably,located in a position that is approximately 7 nucleotides from the TATAbox of the promoter, or promoter fragment, plus one or more full turnsof DNA helix. The expression cassettes may further comprise a secondpromoter operatively linked to a nucleic acid sequence that encodes apolypeptide, which comprises an amino acid sequence selected from thegroup consisting of: (i) SEQ ID NO:4; (ii) SEQ ID NO:5; (iii) SEQ IDNO:6; and (iv) sequences that are substantially similar to either SEQ IDNO:4, 5 or 6.

In a related embodiment, the invention provides plant gene expressioncassettes similar to those described above, wherein the expression ofthe second promoter is capable of being chemically-induced. Accordingly,expression of the nucleic acid sequence to which the second promoter isoperatively linked is stimulated or enhanced by applying an effectiveamount of the chemical inducer to the plant cells, embryos, or tissuesthat have been transformed with the expression cassette of the presentinvention.

In a further embodiment, the present invention provides plant geneexpression cassettes comprising (i) a first promoter, which comprises anucleic acid sequence that is capable of interacting with at least oneDNA-binding domain of at least one polypeptide, operatively linked to agene of interest and (ii) a second promoter operatively linked to anucleic acid sequence that encodes a polypeptide, which comprises anamino acid sequence that is at least substantially similar to SEQ IDNO:6 and a DNA-binding domain that is capable of interacting with thecorresponding nucleic acid sequence of the first promoter. In a relatedembodiment, the present invention provides that the expression of thesecond promoter may be chemically-induced.

In other embodiments, novel transcription factors and uses thereof areprovided. In particular, the inventors have discovered that the acidicdomain of RF2a (SEQ ID NO:6), and sequences substantially similar to SEQID NO:6, can be fused to unrelated transcription factors, ortranscription factor-like complexes, to regulate gene expression. Morespecifically, the invention provides that novel transcription factors,which comprise the acidic domain of RF2a and at least one DNA-bindingdomain, can be used to modulate the expression of one or more genes ofinterest, which are driven by promoters that comprise nucleic acidsequences recognized by the at least one DNA-binding domain of suchnovel transcription factors.

In other embodiments, the invention provides methods of regulating theexpression level of at least one gene of interest comprisingtransforming a plant cell with at least one plant gene expressioncassette of the present invention. Still further, the invention providesmethods of regulating the expression level of at least one gene ofinterest comprising (a) transforming plant cells with at least one plantgene expression cassette of the present invention, wherein the cassettecomprises a chemically-inducible promoter operatively linked to anucleic acid sequence that encodes a polypeptide comprising (i) an aminoacid sequence that is at least substantially similar to SEQ ID NO:6 and(ii) an amino acid sequence that is capable of interacting with anotherpromoter operatively linked to a gene of interest, wherein theinteraction initiates and/or enhances the expression of the gene ofinterest and (b) contacting plant cells, embryos, tissues, roots, etc.,directly or indirectly, derived from the transformed plant cells with anactivating amount of the expression-inducing chemical.

In other embodiments, the invention provides that two or more chimericpromoters containing the Box II element and/or its operationalderivatives, which are operatively linked to one or more genes ofinterest, can be used in connection with RF2a- and/or RF2b-encodingsequences to achieve a “cascade-type” system. In this embodiment, theexpression of RF2a and/or RF2b activates and/or enhances the expressionof the nucleic acid sequences to which the one or more chimericpromoters are operatively linked. Still further, the nucleic acidsequence encoding the RF2a and/or RF2b protein may be operably linked toa chemically-inducible promoter. In such embodiment, upon contactingplant cells, embryos, or tissues, which have been transformed with suchnucleic acid sequences, with the expression-inducing chemical, the RF2aand/or RF2b transcription factor is produced and subsequently interactswith the Box II element and/or its operational derivatives to regulategene expression. This interaction, of course, results in thesynchronized activation or enhancement of expression of all BoxII-dependent genes (or all genes operatively linked to promoterscontaining operational derivatives of Box II).

In other embodiments, the invention provides that at least one chimericpromoter containing the Box II element and/or its operationalderivatives, which is operatively linked to one or more genes ofinterest, can be used in combination with RF2a- and/or RF2B-encodingsequences to “turn-off” or modulate the expression of one or moreunrelated endogenous and/or exogenous genes of interest. The foregoingcombination, for example, can be used to activate or enhance theexpression of particular sequences that encode molecules thatselectively hybridize to specific target nucleic acid sequences. Thehybridization of an oligomeric compound, for example, with its targetnucleic acid sequence can have the effect of interfering with the normalfunction of the target sequence (this effect is generally referred to as“antisense”). The functions of DNA that can be affected in thisembodiment, for example, include replication and transcription. Thefunctions of RNA that can be affected include translocation of the RNAto the site of protein translation, translation of protein from the RNA,splicing of the RNA to yield one or more mRNA species, and catalyticactivity that may be imparted or facilitated by the RNA. The effect ofsuch interference with target nucleic acid function may provide theability to modulate the expression of particular gene products.

In yet a further embodiment, the invention provides plant cells, plantembryos, plant tissues, whole plants and seeds that have beentransformed with at least one plant gene expression cassette of thepresent invention.

The above-mentioned and additional features of the present invention arefurther illustrated in the Detailed Description contained herein. Allreferences disclosed herein, including U.S. patents, are herebyincorporated by reference in their entirety as if each was incorporatedindividually.

DESCRIPTION OF THE FIGURES

FIG. 1: Comparison of RTBV promoter activity with different constitutivepromoters in BY-2 protoplasts. “RTBV” represents the promoter of RTBV;“E” represents the E fragment of the RTBV promoter; “35S” refers to theenhanced 35S promoter of CaMV; “35S(−46)” refers to the 5′ deletionmutation of the CaMV 35S promoter, which ends at position 46 asdescribed herein; “CsVMV” represents the promoter of CsVMV. The resultspresented are the mean value of three independent experiments withstandard variations. Each experiment included three repeats and all datawere normalized against GFP as internal control.

FIG. 2: Relative GUS activity of each plasmid driven by truncatedmutants of the RTBV promoter. The results presented are the mean valueof three independent experiments. Each experiment includes three repeatsand all data were normalized against GFP as internal control.

FIG. 3: Diagram of constructs that were prepared with the Box II elementinserted into different locations in the context of the E fragment ofthe RTBV promoter. The modified promoters were then inserted into avector, wherein the modified promoters were operatively linked to theuidA coding sequence and Nos terminator. The names of derived plasmidsare shown to the right side of each diagram.

FIG. 4: Activities of the modified promoters shown in FIG. 3. Theresults presented are the mean value of three independent experimentswith standard variation. Each experiment included three repeats and alldata were normalized against GFP as internal control.

FIG. 5: E fragment of the RTBV promoter was activated in tobacco BY-2protoplasts by co-transfection of E::GUS with CsVMV::RF2b; CaMV35S::RF2a and CaMV 35S::RF2a/CsVMV::RF2b.

FIG. 6: Sequences of wild type Box II (labeled Box II) and twonon-limiting examples of its operational derivatives (labeled as BoxIIm1 and Box IIm2). The mutated nucleotides in each operationalderivative are identified in bold underline.

FIG. 7: Relative GUS activity of constructs pE(IIm1)::GUS, pE(IIm2)::GUSand pE::GUS in BY-2 protoplasts as described herein. pE(IIm1) comprisedthe E fragment, wherein the wild type Box II was replaced with the BoxIIm1 element; pE(IIm2) comprised the E fragment, wherein the wild typeBox II was replaced with the Box IIm2 element; pE comprised the Efragment and the wild type Box II element; and the bar labeled “BY-2”represents non-transgenic protoplasts.

FIG. 8: Comparative analysis of DNA binding affinities of RF2a and RF2b.

FIG. 9: The pE(Box IIm1):GUS construct was co-transfected into tobaccoBY-2 protoplasts with CsVMV::RF2b, CaMV 35S::RF2a and35S::RF2a/CsVMV::RF2b. All samples were normalized with GFP internalcontrol.

FIG. 10: The pE(Box IIm2):GUS construct was co-transfected into tobaccoBY-2 protoplasts with CsVMV::RF2b, CaMV 35S::RF2a and CaMV35S::RF2a/CsVMV::RF2b. All samples were normalized with GFP internalcontrol.

FIG. 11: Diagram of Box II and CaMV 35S chimeric promoters (andcontrol). The chimeric promoters were ligated with a plasmid cassettethat contained the uidA coding sequence followed by a Nos terminator.The names of the derived plasmids are shown to the right side of thediagram. The positions of Box II in the various constructs are inrelation to the site of transcription initiation (“+1”).

FIG. 12: Primers used in generating the chimeric promoters containingthe Box II element and portions of the CaMV 35S promoter, which areillustrated in FIG. 11. To facilitate the cloning process, a HindIIIrestriction site was added to the 5′ end of the primers (underlined).Box II elements are shown in bold and upper case letters. The sequencesfrom the CaMV 35S promoter are shown in lowercase italic letters.

FIG. 13: Relative GUS activities in non-transgenic BY-2 protoplasts ofconstructs in which uidA was driven by promoters that comprised Box IIand portions of the CaMV 35S promoter, which are illustrated in FIG. 11.The GUS activity of each sample was normalized against the GFP internalcontrol.

FIG. 14: A: Relative GUS activities of constructs in which the uidA genewas driven by Box II and CaMV 35S fusion promoters (which areillustrated in FIG. 11), wherein the constructs were inserted into BY-2protoplasts that produce RF2a. B: Relative GUS activities of theconstructs referenced in (A) above, wherein the constructs were insertedinto BY-2 protoplasts that produce RF2a and RF2b. The GUS activity ofeach sample was normalized against the GFP internal control.

FIG. 15: A: Diagram of the T-DNA regions of binary plasmids used forAgrobacterium-mediated transformation of Arabidopsis. B: GUS activity ofT₁ transgenic Arabidopsis plants. The results present the mean value ofat least 15 independent transgenic plants. The relative GUS activity wascalculated by comparison with E::GUS (=1).

FIG. 16: Electrophoretic mobility shift assay of protein-DNA complexesformed between mutants of RF2a and the Box II element. A: Schematicdiagram of mutants of RF2a. “A” represents the acidic domain; “P”represents the proline-rich domain; and “Q” represents theglutamine-rich domain. B: SDS-PAGE analysis of the purified RF2a mutantproteins. C: Gel mobility shift assay using purified mutant proteins ofRF2a as labeled. A control lane without protein (labeled “Free”) wasincluded in the assay. Box IIm1 DNA was labeled with ³²P, andradioactivity was detected by autoradiography.

FIG. 17: Effects of RF2a and mutants of RF2a on gene expression in BY-2protoplasts. A: Reporter and effector gene constructs. The GUS reportergene (uidA sequence) was driven by a promoter that comprised the Box IIelement operatively linked to nucleotides −48 to +8 of the CaMV 35Spromoter, and was followed by a nopaline synthase 3′ terminator sequence(“pBII-48Ca:GUS”). Effectors included sequences encoding RF2a and RF2amutants operatively linked to the CaMV 35S promoter and nopalinesynthase terminator. B: Relative GUS activities in BY-2 protoplasts thatwere co-transfected with Reporter and Effector gene constructs describedherein. The results represent the averages of detected GUS activities(with S.D.) of three independent experiments, three samples perexperiment, after normalization with GFP.

FIG. 18: The effects of RF2a domains on gene expression when in fusionwith the 2C7 DNA-binding domain. A: Diagram of reporter and effectorconstructs used for transient assays involving fusion proteins of RF2afunctional domains with the 2C7 synthetic zinc finger DNA-bindingdomain. B: Relative GUS activities in BY-2 protoplasts that wereco-transfected with the reporter and effector gene constructs asindicated herein. The results represent the averages (with S.D.) ofthree independent experiments, three samples per experiment, afternormalization with GFP.

FIG. 19: Impact of RF2a and RF2a mutants on development of transgenictobacco plants. A: Two-month old transgenic tobacco plants with RF2a andmutants of RF2a driven by the 35S promoter were grown under greenhouseconditions. Only transgenic plants with mutants lacking the acidicdomain (RF2a-ΔPΔA and RF2a-3Δ) showed severe stunting phenotype. B:Transgenic plants at 105 days. Leaves of plants with RF2a-ΔPΔA andRF2a-3Δ were curved downward, and flowering time was significantlydelayed. C: Panel 1: Transversal section of the stem of transgenicplants with RF2a-ΔPΔA in low magnification; Panel 2-4: Transversesections of the lower part of stems of two-month old tobacco plantsstained with toluidine blue O. Panel 2, transgenic plant with RF2a-ΔPΔA.Panel 3, transgenic plant with RF2a-3A. Panel 4, Non-transgenic plant.

FIG. 20: Correlation between severity of abnormal phenotypes shown inFIG. 19 and accumulation of RF2a-ΔPΔA. Severity of the abnormalphenotype of transgenic tobacco plants was marked with “+++” forstunting and “++++” for severe stunted phenotype, whereas “−” indicatesthat no abnormal phenotype was observed. Upper panel, 40-μg proteinsamples were separated by 10% SDS-PAGE and detected with antibodyagainst full-length RF2a after blotting to nitrocellulose membrane. Theband that contains RF2a-ΔPΔA is marked on the right. Lower panel, themembrane used in the immunoblot was stained with Ponceau S (SigmaChemical Company, St. Louis, Mo.) prior to the antibody reaction.

FIG. 21: Activation of GUS expression in non-vascular tissues byinduction of RF2a. Leaf tissues from transgenic Arabidopsis plants werestained in buffer containing X-Gluc to detect GUS expression. Thetransgenic Arabidopsis plants (shown at the top of FIG. 21) included theE:GUS, 5G35m:RF2a, and Cs:VGE cassettes described herein. “Treated” leaftissue was subjected to applications of Intrepid® 2F as describedherein, whereas “Untreated” leaf tissue was not subjected to Intrepid®2F. The shaded leaf tissue in the “Treated” leaf correlates with the GUSexpression pattern observed. Leaf tissue transformed with only E:GUS isshown at the bottom of FIG. 21.

FIG. 22: Quantitative analysis of the activation of the E fragment byRF2a upon chemical induction. A: Relative GUS activity of T₂ transgenicArabidopsis plants, which comprise the E:GUS, 5G35Sm:RF2a, and Cs:VGEsequences described herein. Each set of bars represents 1 of 12 groupsof transgenic plant lines, namely, EGaV-3, EGaV-5, EGaV-17, EGaV-31,EGaV-50, EGaV-51, EGaV-56, EGaV-59, EGaV-63, EGaV-70, EGaV-72, andE:GUS. Each bar represents the average of three repeats, three plantsfor each repeat (with standard deviation). Open bars represent controlleaf tissue that was not subjected to Intrepid 2F® treatment. Solid barsrepresent leaf tissue treated with 1:8,000 dilution of Intrepid® 2F. B:Western Blot showing expression of RF2a in a limited number of samplesanalyzed in FIG. 22A. The lower panel shows the SDS-PAGE gel describedbelow, whereas the upper panel shows the detected RF2a protein on thenitrocellulose membrane. The mark “−” refers to control leaf tissue thatwas not treated with Intrepid® 2F, whereas “+” refers to leaf tissuethat was treated with 1:8,000 dilution of Intrepid® 2F. The RF2a-arrowindicates the band position of the RF2a protein.

FIG. 23: Results showing the expression-enhancing activity of variousfragments of the acidic domain of RF2a as further described in Example14.

DESCRIPTION OF THE SEQUENCE LISTING

SEQ ID NO. 1: The nucleic acid sequence of the Box II element.

SEQ ID NO. 2: The nucleic acid sequence of the Box IIm1 element—anoperational derivative of the Box II element.

SEQ ID NO. 3: The nucleic acid sequence of the Box IIm2 element—anoperational derivative of the Box II element.

SEQ ID NO. 4: The amino acid sequence of the RF2a transcription factor.

SEQ ID NO. 5: The amino acid sequence of the RF2b transcription factor.

SEQ ID NO. 6: The amino acid sequence of the acidic domain of the RF2atranscription factor.

SEQ ID NO. 7: Non-limiting example of nucleic acid sequence that encodesthe RF2a transcription factor.

SEQ ID NO. 8: Non-limiting example of nucleic acid sequence that encodesthe RF2b transcription factor.

SEQ ID NO. 9: Non-limiting example of nucleic acid sequence that encodesthe acidic domain of the RF2a transcription factor.

SEQ ID NO. 10: Primer sequence of BoxII-deI-3′.

SEQ ID NO. 11: Primer sequence of BoxII-deI-5′.

SEQ ID NO. 12: The nucleic acid sequence of the E fragment (promoter) ofthe RTBV promoter sequence.

SEQ ID NO. 13-35: Primer sequences referenced in Table 1/Example 2.

SEQ ID NO. 36: The GUS 3′ primer.

SEQ ID NO. 37-42: Primer sequences referenced in Table 2/Example 6.

SEQ ID NO. 43: Control primer 1.5h-53CaMV-c.

SEQ ID NO. 44: Control primer −3.5h-74CaMV-c.

SEQ ID NO. 45: Control primer −5.5h-95CaMV-c.

SEQ ID NO. 46-52: Primer sequences referenced in Table 3/Example 8.

SEQ ID NO. 53: Primer sequence of BII-48Ca 5′.

SEQ ID NO. 54: The amino acid sequence of the proline-rich domain of theRF2a transcription factor.

SEQ ID NO. 55: The amino acid sequence of the glutamine-rich domain ofthe RF2a transcription factor.

SEQ ID NO. 56-61: Primer sequences referenced in Table 4/Example 10.

SEQ ID NO. 62: Nucleic acid sequence of the RTBV promoter.

SEQ ID NO. 63: Nucleic acid sequence of the E fragment containing theBox IIm1 element.

SEQ ID NO. 64: Nucleic acid sequence of the E fragment containing theBox IIm2 element.

SEQ ID NO. 65: Nucleic acid sequence of E(ΔBox II) fragment.

SEQ ID NO. 66: Nucleic acid sequence of the CaMV 35S minimal (1-108)promoter.

SEQ ID NO. 67: Nucleic acid sequence of the CsVMV promoter.

SEQ ID NO. 68: Amino acid sequence of RF2a-ΔP.

SEQ ID NO. 69: Amino acid sequence of RF2a-ΔQ.

SEQ ID NO. 70: Amino acid sequence of RF2a-ΔPΔA.

SEQ ID NO. 71: Amino acid sequence of RF2a-ΔPΔQ.

SEQ ID NO. 72: Amino acid sequence of RF2a-3Δ.

SEQ ID NO. 73: “R”—Reverse Primer sequence.

SEQ ID NO. 74: Nucleic acid sequence of the 2C7 cis element.

SEQ ID NO. 75: Amino acid sequence of the synthetic 2C7 domain.

SEQ ID NO. 76: Nucleic acid sequence used to express the 2C7 domain (SEQID NO. 75).

SEQ ID NO. 77-83: DNA cis elements referenced in Table 5/Example 12.

SEQ ID NO. 84-91: DNA binding domains and related cis elementsreferenced in Table 6/Example 12.

SEQ ID NO. 92: Nucleic acid sequence of chimeric promoter with Gal4 DNAbinding sites and CaMV 35S minimal promoter.

SEQ ID NO. 93: Nucleic acid coding sequence of VGE.

DETAILED DESCRIPTION OF THE INVENTION

The following will describe in detail several preferred embodiments ofthe invention. These embodiments are provided by way of explanationonly, and thus, should not unduly restrict the scope of the invention.In fact, those of ordinary skill in the art will appreciate upon readingthe present specification and viewing the present drawings that manyvariations and modifications of the invention may be employed, used andmade without departing from the scope and spirit of the invention.

The present invention can be viewed as having at least two components.The first of the at least two components relates to the Box II element;operational derivatives of the Box II element; chimeric promoterscontaining one or more of these elements; plant gene expressioncassettes containing at least one chimeric promoter of the presentinvention; plant cells, embryos and tissues transformed with at leastone expression cassette of the present invention and methods of usingthe foregoing compositions in connection with RF2a and/or RF2b toregulate the expression of at least one gene of interest. The second ofthe at least two components relates to (i) novel transcription factorsthat comprise at least one DNA-binding domain and an amino acid sequencethat is at least substantially similar to the acidic domain of RF2a and(ii) methods of using the novel transcription factors to regulate theexpression of at least one gene of interest.

Novel Chimeric Promoters

In one preferred embodiment, the invention provides novel chimericpromoters. The promoters of the present invention comprise a firstnucleic acid sequence derived from any promoter (other than the RTBVpromoter (SEQ ID NO:62)), or promoter fragment, that is capable ofdriving gene expression in plant cells. The promoters further compriseat least one nucleic acid sequence selected from the group consistingof: (i) the Box II element (SEQ ID NO:1); (ii) the Box IIm1 element (SEQID NO:2); (iii) the Box IIm2 element (SEQ ID NO:3); (iv) sequences thatare substantially similar to either SEQ ID NO:1, 2 or 3, or (v) otheroperational derivatives of the Box II element. As used herein, the term“operational derivative” shall refer, generally, to the Box IIm1element, the Box IIm2 element, sequences that are substantially similarto the Box II, Box IIm1 or Box IIm2 element and other nucleic acidsequences that are capable of interacting with RF2a and/or RF2b toregulate gene expression.

It will be understood by those skilled in the art that two nucleic acidsequences are “substantially similar” when approximately 70% or more(preferably at least about 80%, and most preferably at least about 90%or 95%) of the nucleotides match over the defined length of the nucleicacid sequence. Sequences that are substantially homologous can beidentified by comparing the sequences using readily accessible computersoftware, or in a Southern hybridization experiment under, for example,stringent conditions as defined for that particular system. Definingappropriate hybridization conditions for a particular system is withinthe skill of the art. It will be further understood by those skilled inthe art that the phrase “at least substantially similar” refers tosequences that are “substantially similar” as described above or,alternatively, identical to one another.

As used herein, “substantially similar” is further meant to include anucleic acid sequence which, by virtue of the degeneracy of the geneticcode, is not identical with that shown in any of the sequences shown inthe Sequence Listing, but which still encodes the same amino acidsequence; or a modified nucleic acid sequence that encodes a differentamino acid sequence that retains substantially the same activities ofthe original proteins, either because one amino acid is replaced with asimilar amino acid, or because the change (whether it be substitution,deletion or insertion) does not affect the active site of the protein.Thus, it is contemplated by the inventors that various changes may bemade in the nucleic acid sequences disclosed, and, of course, theencoded polypeptides, without appreciable loss of their biologicalactivity or utility in the present invention.

The chimeric promoters of the present invention are, preferably,constructed by combining the first nucleic acid sequence derived fromany plant functional promoter, or promoter fragment, with at least onenucleic acid sequence selected from the group consisting of SEQ ID NO:1,2, 3 and sequences substantially similar to SEQ ID NO:1, 2 or 3. Morepreferably, however, the chimeric promoters of the present invention areconstructed by combining the first nucleic acid sequence derived fromany plant functional promoter, or promoter fragment, with at least onenucleic acid sequence selected from the group consisting of SEQ ID NO:1,2 and 3. The term “chimeric promoter,” as used herein, refers to anyplant functional promoter sequence, or promoter fragment, that comprisesSEQ ID NO:1, 2, 3, or sequences substantially similar thereto, whereinsuch plant functional promoter sequence is not derived from the RTBVpromoter.

The nucleic acid sequences consisting of SEQ ID NO:1, 2, 3, andsequences substantially similar thereto, may be positioned within thefirst nucleic acid sequence described above, which comprises any plantfunctional promoter (or promoter fragment). Alternatively, the nucleicacid sequences consisting of SEQ ID NO:1, 2, 3, and sequences that aresubstantially similar to SEQ ID NO:1, 2 or 3, may be fused to the 5′ or3′ end of such plant functional promoter (or promoter fragment).

Although SEQ ID NO:1, 2, 3, and sequences substantially similar thereto,may be positioned within, or fused to the end of, a chimeric promoter,such sequences are, preferably, positioned in specific locations of theDNA helix. In particular, such nucleic acid sequences are, preferably,operably linked to the 5′ end of the selected promoter, or promoterfragment, with a space of approximately 7 nucleotides from the TATA boxplus one or more full “turns of DNA helix.” It is well-known in the artthat one turn of DNA helix equals, approximately, 10.4 base pairs.Furthermore, the TATA box, which, generally, is the module within apromoter that functions to position the start site for RNA synthesis,and its location in a promoter can be easily identified by those skilledin the art. In many cases, the TATA box consensus sequence (TATAAT) is20 to 30 base pairs upstream (i.e., 5′) of the transcription start site(by convention −30 to −20 base pairs relative to the transcription startsite).

The Box II element and its operational derivatives may be used inconnection with a variety of promoters, or promoter fragments, to createnovel chimeric promoters. Preferably, however, the Box II element and/orits operational derivatives are operably linked to a promoter, orpromoter fragment, that comprises a transcription initiation domain. Theterm “transcription initiation domain” refers to a sequence having atleast an RNA polymerase binding site and an mRNA initiation site.

Such basic guidelines for promoter, or promoter fragment, selectionemphasize the notion that the Box II element and its operationalderivatives are, indeed, “portable” and can be transferred to aplurality of promoter sequences. Of course, the promoter sequence withwhich the Box II element and/or its operational derivatives will beused, preferably, relates to the target cell-type in which geneexpression is desired.

For example, some promoters are known to be active in particularcell-types, in certain tissues, under certain abiotic conditions and/orin the presence of certain inducible agents. Thus, the cell-type and/orconditions in which gene expression is desired will impact the identityof the promoter sequence with which Box II and/or its operationalderivatives will be used. Although the endogenous promoter of the geneof interest may be utilized herein for transcriptional regulation,preferably, the promoter is a foreign regulatory sequence. For plantexpression vectors, suitable viral promoters include, for example, theRTBV promoter; the 35S RNA and 19S RNA promoters of the cauliflowermosaic virus (“CaMV”); the full-length transcript promoter from figwortmosaic virus (“FMV”); and the cassaya vein mosaic virus (“CsVMV”)promoter.

The Box II element, of course, can be isolated from natural sources,e.g., the Box II element can be isolated from the E fragment of the RTBVpromoter (SEQ ID NO:62) using techniques well-known the art. Morepreferably, however, the Box II element and its operational derivatesare synthesized using standard DNA synthesis techniques (see, forexample, Current Protocols in Molecular Biology, Unit 2.11, eds.Ausubel, et al., John Wiley & Sons, 1995).

Expression Cassettes Comprising Novel Chimeric Promoters

The present invention further provides plant gene expression cassettesthat comprise a first chimeric promoter of the present inventionoperatively linked to one or more genes of interest. The expressioncassettes may further comprise a second promoter operatively linked to anucleic acid sequence that encodes a polypepide, which comprises anamino acid sequence selected from the group consisting of: (a) SEQ IDNO:4; (b) SEQ ID NO:5; (c) SEQ ID NO:6 and (d) sequences that aresubstantially similar to either SEQ ID NO:4, 5 or 6. Non-limitingexamples of nucleic acid sequences that encode the amino acid sequencesset forth in SEQ ID NO:4, SEQ ID NO:5 and SEQ ID NO:6 are shown in SEQID NO:7, SEQ ID NO:8 and SEQ ID NO:9, respectively.

The one or more genes of interest operatively linked to a first chimericpromoter of the present invention, when including an open reading frame(“ORF”), may encode a protein. Of course, the gene of interest can be anendogenous or exogenous sequence. In addition, the ORF may includecertain 5′ and 3′ untranslated sequences. Still further, appropriatetranscription termination and polyadenylation sequences may, preferably,be included.

Genes of interest, the expression of which may be regulated according tothe present invention, may include, for example, sequences thatnaturally exist in plants, animals, bacteria, viruses or fungi;synthetic DNA sequences that encode a specific RNA or protein product;cDNA sequences derived from mRNA; DNA sequences modified by mutagenesis,for example, through site specific mutagenesis; chimeras of any of theabove (to produce fusion proteins); and DNA sequences encodingcomplementary RNA molecules (for “antisense” applications); andcombinations and/or fragments of the above.

Examples of proteins that can be encoded by the gene of interestinclude, but are not limited to, nutritionally important proteins;growth promoting factors; proteins for early flowering in plants;proteins that impart protection to the plant under certain environmentalconditions, e.g., proteins conferring resistance to metals or othertoxic substances, such as herbicides or pesticides; stress relatedproteins that confer tolerance to temperature or hydration extremes;proteins conferring resistance to fungi, bacteria, viruses, insects andnematodes; and proteins of specific commercial value, e.g., enzymesinvolved in metabolic pathways, proteins having therapeutic activity inhumans, and others.

The term “operably linked,” as used herein, refers to the functionallinkage between, for example, the Box II element and/or its operationalderivatives and a plant functional promoter or promoter fragment;between a promoter sequence, including the novel chimeric promoters ofthe present invention, and any gene of interest; and between a promotersequence and any sequence encoding the RF2a protein, RF2b protein, aprotein comprising the acidic domain of RF2a and/or any protein that issubstantially similar to the foregoing proteins.

The second promoter operatively linked to a nucleic acid sequence thatencodes a polypepide, which comprises an amino acid sequence selectedfrom the group consisting of: (a) SEQ ID NO:4; (b) SEQ ID NO:5; (c) SEQID NO:6; and (d) sequences that are substantially similar to either SEQID NO:4, 5, or 6, may constitute any promoter that is capable of drivinggene expression in the target plant cells. As described above, certainpromoters are known to be active in particular cell-types, in certaintissues, under certain abiotic conditions and/or in the presence ofcertain inducible agents. Thus, the cell-type and/or conditions in whichgene expression is desired will impact the identity of the promoter thatis selected to drive expression of sequences encoding RF2a, RF2b,polypeptides comprising the acidic domain of RF2a or polypeptides thatare substantially similar to any of the foregoing. Of course, suchpromoters may include both constitutive, e.g., the CaMV promoters, andinducible promoters.

By placing the nucleic acid sequence encoding RF2a, RF2b, polypeptidescomprising the acidic domain of RF2a or polypeptides that aresubstantially similar to any of the foregoing, under the control of achemically-inducible promoter, the gene expression system can beactivated at will. The use of inducible promoters in this capacityprovides control over the effect that the encoded proteins may have onthe expression of promoter sequences (and genes operatively linked tosuch sequences) comprising the Box II element and/or its operationalderivatives. In short, expression of the nucleic acid sequence to whichthe second promoter is operatively linked is stimulated and/or enhancedby applying an effective amount of the chemical inducer to the plantcells, embryos or tissues that have been transformed with theappropriate expression cassette of the present invention. Application ofthe inducer, therefore, allows the expressed transcription factor tointeract with, and stimulate (or enhance) the expression of, thechimeric promoter and the one or more genes of interest to which it isoperatively linked.

To be most useful, an inducible promoter should 1) provide lowexpression in the absence of the inducer; 2) provide high expression inthe presence of the inducer; 3) employ an induction scheme that does notinterfere with the normal physiology of the plant; and 4) has no effecton the expression of other genes. Examples of inducible expressionschemes useful in plants include those induced by chemical means, suchas the ecdysone agonist-inducible gene expression systems(Christopherson et al., 1992; Martinez et al., 1999). The ecdysoneagonist-inducible gene expression systems, preferably, employcommercially-available non-steroidal ecdysone agonists, such astebufenozide and methoxyfenozide.

Additional examples of inducible promoters useful in plants include, butare not limited to, promoters that respond to tetracycline (Gatz et al.,1992; Weinmann et al., 1994); the yeast metallothionein promoter, whichis activated by copper ions; the In2-1 and In2-2 regulator sequences,which are activated by substituted benzenesulfonamides, e.g., herbicidesafeners; and GRE regulatory sequences, which are induced byglucocorticoids. In addition, plant promoters such as thelight-inducible promoter from the small subunit of ribulose bis-phospatecarboxylase (ssRUBISCO); mannopine synthase promoter; nopaline synthase(“NOS”) and octopine synthase (“OCS”) promoters (carried ontumor-inducing plasmids of Agrobacterium tumefaciens) or heat shockpromoters, e.g., soybean hsp17.5-E or hsp17.3-B, may be used. Otherpromoters, both constitutive and inducible, will be known to those ofskill in the art.

It will be appreciated by those skilled in the art that the firstchimeric promoter, which is operatively linked to at least one gene ofinterest, and the second promoter, which is operatively linked to asequence encoding RF2a, RF2b, polypeptides comprising the acidic domainof RF2a or polypeptides that are substantially similar to any of theforegoing, may exist in a single gene expression cassette (or vector),or, alternatively, in separate cassettes (or vectors). Still further,those skilled in the art will appreciate that an expression cassette maycomprise a single chimeric promoter, or, alternatively, a plurality ofchimeric promoters, each operatively linked to at least one gene ofinterest. Moreover, the plurality of chimeric promoters may besubstantially similar in sequence, or, alternatively, may comprisesignificantly different sequences.

Novel Transcription Factors

Over the years, several classes of DNA-binding proteins have beencharacterized and the nucleic acid sequences with which such proteinsinteract identified. For example, zinc finger proteins represent a classof motifs that are known to be involved in the sequence-specificrecognition of DNA. As the name implies, this DNA-binding domain isfolded around a zinc ion. To date, more than two hundred proteins, manyof them transcription factors, have been shown to possess zinc fingerdomains. In general, zinc fingers connect transcription factors to theirtarget locations by binding to specific DNA sequences.

The RF2a and RF2b transcription factors described herein represent yetanother class of DNA-binding proteins. Specifically, RF2a and RF2b arerepresentative examples of what are commonly referred to as bZIPtranscription factors. The bZIP transcription factors are generallycharacterized by a bipartite DNA-binding domain consisting of a basicregion involved in sequence-specific binding, and a leucine zipperregion required for dimerization. The bZIP domain of RF2a shares highsimilarity with bZIP proteins that exist naturally in plants such asArabidopsis, tobacco, tomato, and other plants (Fukazawa et al., 2000;Jakoby et al., 2002; Ringli and Keller, 1998). In particular, this groupof proteins is known to have a lysine residue at the −10 positionrelative to the first leucine residue of the leucine zipper region (Yinet al., 1997). The amino acid sequence signature of the DNA-bindingregions of this class of proteins is NXXXSAXXSK (Fujii et al., 2000).

The present invention provides novel transcription factors, and usesthereof, which provide the ability to regulate the expression of atleast one gene of interest. In particular, the inventors have discoveredthat the acidic domain of RF2a (SEQ ID NO:6), and amino acid sequencessubstantially similar to SEQ ID NO:6, can be fused to unrelatedtranscription factors, or transcription factor-like complexes, toregulate gene expression. In certain embodiments, the invention providesthat novel transcription factors, which comprise the acidic domain ofRF2a and at least one DNA-binding domain, can be used to modulate theexpression of one or more genes driven by promoters that comprisenucleic acid sequences recognized by such DNA-binding domain of thenovel transcription factors.

In certain embodiments, the acidic domain of RF2a (SEQ ID NO:6), and/oramino acid sequences substantially similar to SEQ ID NO:6, can be fusedto any class of DNA-binding domains (and/or unrelated transcriptionfactors comprising such domains). The acidic domain of RF2a, and/orsubstantially similar sequences, can be fused, for example, to anypolypeptide comprising a leucine zipper, bZIP domain, zinc-finger,homeobox, basic helix-loop-helix domain, or other DNA-binding domainscurrently known in the art (or discovered hereafter). It should beappreciated, however, that the DNA-binding domain selected (or thepolypeptide comprising such domain) must be capable of interacting withthe promoter operatively linked to the gene of interest for whichcontrol of expression is desired.

It will be appreciated by those skilled in the art that two amino acidsequences are “substantially similar” when approximately 70% or more(preferably at least about 80%, and more preferably at least about 90%or 95%) of the amino acids match over the defined length of thesequences. The term “substantially similar” is further meant to refer toamino acid sequences that have been modified from an original sequence,wherein the modified amino acid sequence retains substantially the samelevel of activity as the original amino acid sequence. This retention inactivity, of course, may occur when one or more amino acids are replacedwith similar amino acids, or because the change (whether it besubstitution, deletion or insertion) does not affect the active site ofthe protein. Thus, it is contemplated by the inventors that variouschanges may be made to the acidic domain of RF2a, without appreciableloss of its biological activity and utility in the present invention. Itwill be further understood by those skilled in the art that the phrase“at least substantially similar” as it is used herein with respect toamino acid sequences refers to sequences that are “substantiallysimilar” as described above or, alternatively, identical to one another.

In certain embodiments, for example, novel transcription factors areprovided, which comprise a fragment of the acidic domain of RF2a (SEQ IDNO:6). More particularly, the present invention contemplates thatinternal regions and fragments of the acidic domain of RF2a (SEQ IDNO:6) may be used to form novel transcription factors, which are capableof regulating gene expression as described herein.

As used herein, “fragments of the acidic domain” and “fragment of theacidic domain” refer to amino acid sequences comprising less than all ofthe amino acid residues of SEQ ID NO:6, wherein such amino acid sequenceis substantially similar to the corresponding region of the full-lengthSEQ ID NO:6. More particularly, for example, a “fragment of the acidicdomain” includes an amino acid sequence encompassing at least 50%, 60%,70%, 80%, or 90% of SEQ ID NO:6, wherein such amino acid sequence issubstantially similar to the corresponding region of the full-length SEQID NO:6.

While the acidic domain of RF2a (SEQ ID NO:6) (and/or amino acidsequences substantially similar to SEQ ID NO:6) and fragments of theacidic domain may be fused to any class of DNA-binding domains (and/orunrelated transcription factors comprising such domains) to create noveltranscription factors as described herein, the invention provides thatsuch sequences may act in the absence of DNA-binding domains to regulategene expression. In such embodiment, the acidic domain of RF2a may beused alone or in connection with other regulatory proteins or domains tomodulate gene expression. For example, the invention provides noveltranscription factors that comprise the acidic domain of RF2a and anyother amino acid sequence not derived from RF2a or RF2b, which arecapable of regulating the expression of at least one gene of interest.The numerous mechanisms by which such transcription factors may regulateexpression are well-known to those skilled in the art, which include,for example, affecting the formation of the transcription initiationcomplex and recruiting other regulatory proteins to the transcriptioninitiation region.

Expression Cassettes Encoding Novel Transcription Factors

The present invention further provides plant gene expression cassettescomprising (i) a first promoter, which comprises a nucleic acid sequencethat is capable of interacting with at least one DNA-binding domain ofat least one polypeptide, operatively linked to a gene of interest and(ii) a second promoter operatively linked to a nucleic acid sequencethat encodes a polypeptide, which comprises an amino acid sequence thatis at least substantially similar to SEQ ID NO:6 and a DNA-bindingdomain that is capable of interacting with the corresponding nucleicacid sequence of the first promoter.

Of course, in light of the foregoing, nucleic acid sequences encodingthe acidic domain of RF2a, and/or substantially similar amino acidsequences, may be operatively linked to, for example, nucleic acidsequences that encode polypeptides comprising any motif known tointeract with the first promoter (or, more specifically, elementscontained within the first promoter), which is operatively linked to theone or more genes of interest. This interaction will, preferably,initiate and/or enhance the expression of the one or more genes ofinterest. An example of a nucleic acid sequence that encodes the acidicdomain of RF2a (SEQ ID NO:6) includes, but is not limited to, thesequence shown in SEQ ID NO:9.

Examples of nucleic acid sequences encoding DNA-binding domains that canbe used in this capacity include, but are not limited to, sequencesencoding a leucine zipper, the bZIP domain, the zinc-finger, thehomeobox, the basic helix-loop-helix domain or others. It will beappreciated by those skilled in the art that the selected DNA-bindingdomain must be capable of interacting with the promoter operativelylinked to the one or more genes of interest for which control ofexpression is desired. Still further, it will be appreciated by thoseskilled in the art that sequences encoding the acidic domain of RF2a,for example, and at least one DNA-binding domain may be tethereddirectly to one another, or, alternatively, may be connected indirectlythrough intervening sequences, e.g., spacers, other polypeptide-encodingsequences, etc.

In certain alternative embodiments, the second promoter is operativelylinked to a nucleic acid sequence that encodes a novel transcriptionfactor, which comprises an amino acid sequence that is at leastsubstantially similar to SEQ ID NO:6 and is capable of modulating theexpression level of the nucleic acid sequence operatively linked to thefirst promoter through means other than direct DNA binding orinteraction. As described above, such transcription factors may be usedto regulate the expression level of one or more genes of interest by,for example, affecting the formation of the transcription initiationcomplex or recruiting other regulatory proteins to the transcriptioninitiation region.

Any promoter, or promoter fragment, capable of driving gene expressionin plant cells may be operatively linked to sequences encoding the noveltranscription factors of the present invention. The promoter selectedfor any given system or application may confer constitutive expressionin the transformed plant cell, or, alternatively, inducible expression.Furthermore, as described above with respect to other embodiments,certain promoters are known to be active in particular cell-types, incertain tissues and/or under certain abiotic conditions. Thus, thecell-type and/or conditions in which gene expression is desired willimpact the identity of the promoter selected to drive expression ofsequences encoding the novel transcription factors of the presentinvention.

Thus, in one embodiment, the nucleic acid sequences encoding the noveltranscription factors of the present invention may be placed under thecontrol of chemically-inducible promoters. In this embodiment, the geneexpression system may be activated at will, which provides control overthe effect that the encoded novel transcription factors may have on theexpression of promoter sequences (and genes operatively linked to suchsequences) that comprise the element to which the expressed DNA-bindingdomain, for example, is capable of interacting. As described above withrespect to other embodiments, several inducible promoters well-known inthe art could be used in this capacity to drive the expression of noveltranscription factors.

It will be appreciated by those skilled in the art that the firstpromoter, which is operatively linked to at least one gene of interest,and the second promoter, which is operatively linked to a sequenceencoding a novel transcription factor of the present invention, mayexist in a single gene expression cassette (or vector), or,alternatively, in separate cassettes (or vectors). Still further, thoseskilled in the art will appreciate that a single promoter, or,alternatively, a plurality of promoters, each operatively linked to atleast one gene of interest, may contain a sequence and/or elementcapable of interacting with the encoded novel transcription factors.Moreover, the plurality of promoters can be substantially similar insequence, or, alternatively, may comprise significantly differentpromoter sequences.

Methods of Regulating Gene Expression

The invention further provides methods of regulating the expressionlevel of at least one gene of interest, which comprise transforming aplant cell with at least one plant gene expression cassette of thepresent invention. Still further, the invention provides methods ofregulating the expression level of at least one gene of interest, whichcomprise (a) constructing at least one plant gene expression cassette ofthe present invention; (b) transforming a plant cell with the plant geneexpression cassette of the present invention; and (c) regenerating wholeplants from the transformed plant cell. In a related embodiment, forplants, plant tissues or plant cells that have been transformed with agene expression cassette comprising a chemically-inducible promoteroperatively linked to a nucleic acid sequence that encodes a polypeptidecomprising an amino acid sequence that is at least substantially similarto SEQ ID NO:4, 5 or 6, the method further comprises contacting thetransformed plants, plant tissues or plant cells, directly orindirectly, with an activating amount of the expression-inducingchemical.

In other embodiments, plant gene expression cassettes comprising two ormore chimeric promoters of the present invention, which are operativelylinked to one or more genes of interest, can be transformed into a plantcell in connection with, for example, RF2a- and/or RF2B-encodingsequences to achieve a “cascade-type” system. In such embodiments, theexpression of RF2a and/or RF2b activates and/or enhances the expressionof the nucleic acid sequences to which the two or more chimericpromoters are operatively linked. Still further, the nucleic acidsequences encoding the RF2a and/or RF2b proteins, for example, may beoperably linked to chemically-inducible promoters. In such case, uponcontacting plants, plant tissues or plant cells, which have beentransformed with such sequences, with the expression-inducing chemical,the RF2a and/or RF2b transcription factors are produced. The RF2a and/orRF2b transcription factors subsequently interact with the Box IIelements (and/or operational derivatives of Box II) to regulate geneexpression. This interaction, of course, results in the synchronizedactivation and/or enhancement of expression of all Box II-dependentgenes (or all genes operatively linked to promoters containingoperational derivatives of Box II).

In other embodiments, plant gene expression cassettes comprising atleast one chimeric promoter of the present invention, which isoperatively linked to one or more genes of interest, can be transformedinto plant cells in connection with RF2a- and/or RF2b-encoding sequencesto “turn-off” or modulate the expression of one or more unrelatedendogenous and/or exogenous genes. The foregoing expression cassettescan be used, for example, to activate and/or enhance the expression ofthe one or more genes of interest that encode molecules that selectivelyhybridize to specific target nucleic acid sequences, e.g., endogenousand/or exogenous genes. The hybridization of an oligomeric compound, forexample, with its target nucleic acid sequence can have the effect ofinterfering with the normal function of the target sequence (this effectis generally referred to as “antisense”). The functions of DNA that canbe affected in this embodiment, for example, include replication andtranscription. The functions of RNA that can be affected include allvital functions such as translocation of the RNA to the site of proteintranslation, translation of protein from the RNA, splicing of the RNA toyield one or more mRNA species, and catalytic activity that may beimparted or facilitated by the RNA. The effect of such interference withtarget nucleic acid function provides the ability to modulate theexpression of particular gene products.

The transformation of plant cells in accordance with the presentinvention may be carried out in essentially any of the various waysknown to those skilled in the art of plant molecular biology. That is,the method employed for transformation of target plant cells is notrelevant to the present invention and any method suitable for the targetplant cell-type may be utilized. As used herein, the term“transformation” refers to the alteration of the genotype of a hostplant, including within plant cells, embryos and tissues, by theintroduction of exogenous or endogenous nucleic acid sequences. Further,the terms “transfection” and “transformation,” as used herein, may beused interchangeably, wherein the meaning accorded to both terms is,generally, as described above with respect to “transformation.”

Neither is the plant species to which the methods and compositions ofthe present invention relate particularly germane to the invention. Forexample, dicotyledonous and monocotyledonous plants can be transformed.Thus, the various embodiments of the present invention may be applied toany plant, plant tissue, seed or plant cell for which transformationtechniques are, or become, available.

In general, to commence a transformation process in accordance with thepresent invention, it is first necessary to construct a suitable vectorand properly introduce the vector into a plant cell. The details of theconstruction of vectors utilized herein are known to those skilled inthe art of plant molecular biology. As described above, one or moreplant gene expression cassettes may be constructed to practice themethods, and to generate the plants, plant tissues and plant cells of,the present invention. In practice, the construct or constructscomprising the expression cassettes of the present invention will beinserted into a plant cell by transformation.

For example, constructs that include chimeric promoters of the presentinvention, which comprise the Box II element and/or its operationalderivatives, can be introduced into plant cells using Ti plasmids,root-inducing (R1) plasmids, and plant virus vectors. In the firstinstance, for example, the nucleic acid sequences of the presentinvention can be introduced into plant cells throughAgrobacterium-mediated transformation. Methods involving the use ofAgrobacterium-mediated transformation include, but are not limitedto: 1) co-cultivation of Agrobacterium with cultured isolatedprotoplasts; 2) transforming (or infecting) plant cells or tissues withtransformed Agrobacterium (as described herein); or 3) transformation ofseeds, explants, apices or meristems with Agrobacterium. Underappropriate conditions known in the art, the transformed plant cells maybe grown to form shoots, roots, and develop further into plants.

In some cases, it may be preferred to introduce the nucleic acidsequences of the present invention into plant cells utilizingAgrobacterium tumefaciens containing the Ti plasmid. When using an A.tumefaciens culture as a transformation vehicle, it is most advantageousto use a non-oncogenic strain of the Agrobacterium as the vector so thatnormal non-oncogenic differentiation of the transformed tissues ispossible. It is also preferred that the Agrobacterium harbor a binary Tiplasmid system. Such a binary system comprises 1) a first Ti plasmidhaving a virulence region essential for the introduction of transfer DNA(T-DNA) into plants and 2) a chimeric plasmid. The chimeric plasmidcontains at least one border region of the T-DNA region of a wild-typeTi plasmid flanking the nucleic acid sequence to be transferred. BinaryTi plasmid systems have been shown to be effective in transforming plantcells.

Alternatively, the nucleic acid sequences of the present invention canbe introduced into plant cells using mechanical or chemical means. Forexample, nucleic acid sequences can be mechanically transferred bydirect microinjection into plant cells utilizing micropipettes. Stillfurther, the nucleic acid sequences may be transferred into plant cellsusing polyethylene glycol, which is capable of forming a precipitationcomplex with nucleic acid sequences that is taken up by target plantcells.

The nucleic acid sequences of the present invention can also beintroduced into plant cells by electroporation. In this technique, plantprotoplasts, for example, are electroporated in the presence of vectorsor nucleic acid sequences to be transformed into the protoplasts.Electrical impulses of high field strength reversibly permeabilize plantmembranes allowing the introduction of nucleic acids. Electroporatedplant protoplasts reform the cell wall, divide and form a plant callus.Selection of the transformed plant cells with the transformed gene canbe accomplished using, for example, phenotypic markers.

Another well-known method for introducing nucleic acid sequences of thepresent invention into plant cells is high velocity BIOLISTIC®penetration by small particles with the nucleic acid sequences to beintroduced contained either within the matrix of small beads orparticles, or on the surface thereof. See, for example, U.S. Pat. Nos.5,932,479 and 5,693,507.

Additionally, DNA viruses may be used as vectors for introducingheterologous nucleic acid sequences into plant cells. See, for example,U.S. Pat. No. 4,407,956. Non-limiting examples of such DNA virusesinclude the Cauliflower mosaic virus (“CaMV”) and the Geminivirus. TheCaMV viral DNA genome, for example, may be inserted into a parentbacterial plasmid creating a recombinant DNA molecule which can bepropagated in bacteria. After cloning, the recombinant plasmid may bere-cloned and further modified by introduction of the desired nucleicacid sequence of the present invention. The modified viral portion ofthe recombinant plasmid is then excised from the parent bacterialplasmid, and used to inoculate the target plant cells.

In any of the foregoing methods of transformation, a selectable markermay, optionally, be associated with constructs comprising nucleic acidsequences of the present invention. As used herein, “marker” refers to agene that encodes a protein that confers a particular trait or aphenotype that permits the selection of, or the screening for, a plantor plant cell containing the marker. In some cases, the marker gene mayencode a protein that confers antibiotic resistance to transformed plantcells, whereby the appropriate antibiotic can be used to select fortransformed plant cells among cells that are not transformed. Examplesof suitable selectable markers include adenosine deaminase,dihydrofolate reductase, hygromycin-B-phosphotransferase, thymidinekinase, xanthine-guanine phosphoribosyltransferase and amino-glycoside3′-O-phosphotransferase II (kanamycin, neomycin and G418 resistance).Other suitable markers will be known to those of skill in the art. Forexample, screenable markers, such as the uidA gene, which encodesβ-glucuronidase (“GUS”), luciferase or the gene encoding the greenfluorescent protein (“GFP”), may also be used.

Plants and Plant Parts

Still further, the invention provides plant cells, plant embryos, planttissues, whole plants and seeds that have been transformed with at leastone plant gene expression cassette of the present invention. Methods ofregenerating whole plants from transformed plant cells, embryos andtissues are well-known to those skilled in the art.

The following Examples are included to demonstrate certain embodimentsof the invention. It should be appreciated by those skilled in the artthat the techniques disclosed in the Examples that follow representtechniques discovered by the inventors to function well in the practiceof the invention, and thus, can be considered to constitute preferredmodes for its practice. However, those of ordinary skill in the artshould, in light of the present disclosure, appreciate that many changescan be made in the specific embodiments that are disclosed and stillobtain a like or similar result without departing from the spirit andscope of the invention.

EXAMPLES Example 1

Analysis of the Box II Sequence in BY-2 Protoplasts

Until now, the behavior of the RTBV promoter in the tobacco BY-2 cellline and the contribution of its various cis elements to the promoteractivity in BY-2 cells was unknown. To compare the relative activity ofthe RTBV promoter with other constitutive promoters, tobacco BY-2protoplasts were transfected with gene constructs in which the uidA openreading frame (“ORF”) was driven by the enhanced cauliflower mosaicvirus (“CaMV”) 35S promoter, the enhanced CaMV promoter with a 5′deletion (at position −46 in relation to the transcription start site),the cassaya vein mosaic virus (“CsVMV”) promoter, the RTBV promoter orthe E fragment of the RTBV promoter. The results are shown in FIG. 1,which indicate that the RTBV promoter and, more particularly, the Efragment of the RTBV promoter exhibit strong activity in BY-2 cells.Specifically, the E fragment exhibited more than one third of theactivity that was observed with the CaMV 35S promoter, which isgenerally considered a strong promoter in plant cells.

To evaluate the functional contribution of different cis elements to theactivity of the RTBV promoter, deletion mutants were generated from theE fragment by removing the GATA motif, ASL box and the Box II element atpositions −−b 100, −68 and −32, respectively. In FIG. 2, “pE” representsthe entire E fragment; “p-100” represents a truncated E fragment atposition −100, which excludes the GATA motif; “p-68” represents atruncated E fragment at position −68, which excludes the GATA motif andASL box; and “p-32” represents a truncated E fragment at position −32,which excludes the GATA motif, ASL box and Box II element. All of theforegoing fragments included the TATA box and Box I element of the RTBVpromoter.

The mutated promoters were then fused with the uidA gene. The GUSexpression levels of the derived plasmids were determined in BY-2protoplasts. The data in FIG. 2 show that the Box II element is crucialfor promoter function in BY-2 protoplasts. As long as the Box II elementwas retained, the minimal promoter exhibited an expression level similarto that of the full E fragment. Once the Box II element was removed,however, the promoter activity decreased to less than 20% of the Efragment.

Example 2

The Optimal Position of the Box II Sequence

The optimal spacing of the Box II element, relative to the TATA box, formaximal effect on expression of the host promoter was determined. Theoriginal Box II sequence was deleted from the RTBV promoter in thecontext of the E fragment and re-inserted into the promoter at differentlocations, as indicated in FIG. 3. The mutated promoters were insertedinto a cassette which contained the uidA coding sequence and Nosterminator. The derived plasmids are illustrated in FIG. 3.

Construction of Plasmids with Relocated Box II in the E promoter—Torelocate the Box II element in the E promoter (fragment), the Box IIelement was first removed from the E promoter using fusion PCR strategyto generate E(ΔBox II). Next, the Box II element was re-introduced backinto E(ΔBox II) (SEQ ID NO:65) at varied positions. In the first PCRreactions, two products were generated using the primer set R (SEQ IDNO:73)/BoxII-deI-3′ (SEQ ID NO:10) and BoxII-deI-5′ (SEQ ID NO:11)/GUS3′(SEQ ID NO:13) with pE:GUS as templates, wherein E represents the Efragment (SEQ ID NO:12) and GUS represents the uidA sequence, which iswell-known in the art. The PCR products were gel purified and then usedas templates for a second PCR reaction employing the R (SEQ IDNO:73)/GUS3′ (SEQ ID NO:13) primer set.

The PCR product from the second reaction was restricted withHindIII/NcoI and cloned into pE:GUS to replace the E promoter with thesame set of restriction sites. The resultant construct was namedpE(ΔBoxII):GUS. The Box II element was re-introduced into pE(ΔBoxII):GUSusing the same fusion PCR strategy as described above. To generate theE-Box II+11, E-Box II-9, E-Box II-17, E-Box II-58, E-Box II-63, E-BoxII-74, E-Box II-79, E-Box II-100, E-Box II-116, E-Box II-147 and E-BoxII-164 promoters, the first PCR reactions were carried out using theprimer sets shown in the following Table 1: TABLE 1 Promoters PrimerSets Respective SEQ ID NOs. E-Box II+11 R/mtEBoxII(−0.5h)-3′ SEQ ID NO:73/14 mtEBox II(−0.5h)-5′/GUS3′ SEQ ID NO: 15/13 E-Box II−9R/mtEBoxII(−1.0h)-3′ SEQ ID NO: 73/16 mtEBoxII(−1.0h)-5′/GUS3′ SEQ IDNO: 17/13 E-Box II−17 R/mtEBoxII(−2.0h)-3′ SEQ ID NO: 73/18mtEBoxII(−2.0h)-5′/GUS3′ SEQ ID NO: 19/13 E-Box II−58R/mtEBoxII(−2.5h)-3′ SEQ ID NO: 73/20 mtEBoxII(−2.5h)-5′/GUS3′ SEQ IDNO: 21/13 E-Box II−63 R/mtEBoxII(−4.5h)-3′ SEQ ID NO: 73/22mtEBoxII(−4.5h)-5′/GUS3′ SEQ ID NO: 23/13 E-Box II−74R/mtEBoxII(−6.0h)-3′ SEQ ID NO: 73/24 mtEBoxII(−6.0h)-5′/GUS3′ SEQ IDNO: 25/13 E-Box II−79 R/mtEBoxII(−9.0h)-3′ SEQ ID NO: 73/26mtEBoxII(−9.0h)-5′/GUS3′ SEQ ID NO: 27/13 E-Box II−100R/mtEBoxII(−111nt)-3′ SEQ ID NO: 73/28 mtEBoxII(−111nt)-5′/GUS3′ SEQ IDNO: 29/13 E-Box II−116 R/mtEBoxII(+2.0h)-3′ SEQ ID NO: 73/30mtEBoxII(+2.0h)-5′/GUS3′ SEQ ID NO: 31/13 E-Box II−147R/mtEBoxII(+29nt)-3′ SEQ ID NO: 73/32 mtEBoxII(+29nt)-5′/GUS3′ SEQ IDNO: 33/13 E-Box II-164 R/mtEBoxII(+6.0h)-3′ SEQ ID NO: 73/34mtEBoxII(+6.0h)-5′/GUS3′ SEQ ID NO: 35/13

The PCR products generated in the first reaction were used as templatesfor the second PCR reaction using R/GUS3′ as primers (SEQ ID NO:73/13).The PCR products from the second reactions were purified and cloned intothe pE:GUS vector to replace the E promoter through the restrictionsites HindIII/NcoI. The resultant plasmids were named pE-BoxII+11:GUS,pE-BoxII-9:GUS, pE-BoxII-17:GUS, pE-BoxII-58:GUS, pE-BoxII-63:GUS,pE-BoxII-74:GUS, pE-BoxII-79:GUS, pE-BoxII-100:GUS, pE-BoxII-116:GUS,pE-BoxII-147:GUS and pE-BoxII-164:GUS, respectively.

BY-2 protoplasts were transfected with the foregoing constructs andtested for GUS activity. Protein samples from such protoplasts wereprepared using protein extraction buffer (Jefferson et al., 1987) andquantified using the DC protein assay kit (Bio-Rad Laboratories,Hercules, Calif.). Quantitative analysis of GUS activity was performedas described by Jefferson et al. (1987) using the substrate4-methylum-belliferyl-β-D-glucuronide (“MUG”) with the Spectra MaxGemini instrument (Molecular Devices Corp., Sunnyvale, Calif.).

As shown in FIG. 4, the E promoter activity dramatically decreased whenthe Box II element was removed (see construct pEΔBoxII). Additionally,when the Box II element was removed and inserted in locations other thanits native location, the mutated promoters exhibited similar activity aspEΔBoxII, which indicates that the position of the Box II element in itsnative promoter is important.

Example 3

Effect of RF2a and RF2b on Expression of a Reporter Gene

As shown in FIG. 1, the E fragment of the RTBV promoter showed strongactivity in tobacco BY-2 protoplasts, presumably because the BY-2 cellline contains RF2a- and RF2b-like transcription factors (Fukazawa etal., 2000). Nevertheless, the E fragment may be further stimulated byco-transfecting the BY-2 protoplasts with constructs that encode theRF2a and/or RF2b transcription factors. In this Example, the E fragmentwas activated in tobacco BY-2 protoplasts by co-transfection of E::GUSwith CsVMV::RF2b, CaMV 35S::RF2a and CaMV 35S::RF2a/CsVMV::RF2b usingmethods well-known in the art. As shown in FIG. 5, the E fragment can beactivated above a strong background expression by over-expression ofRF2a and/or RF2b.

Example 4

Mutants of Box II

To investigate the possibility of reducing the background expressionlevel in BY-2 protoplasts, the activities of certain Box II mutants (or“operational derivatives”), as shown in FIG. 6, were tested in BY-2protoplasts. Specifically, the operational derivatives Box IIm1 (SEQ IDNO:2) and Box IIm2 (SEQ ID NO:3) were tested in the context of the Efragment (SEQ ID NO:63 and SEQ ID NO:64, respectively). The mutatedpromoters were ligated with the uidA coding sequence to create fusiongenes, which are referred to herein as pE(Box IIm1l)::GUS and pE(BoxIIm2)::GUS. BY-2 protoplasts were then transfected with the pE(BoxIIm1)::GUS and pE(Box IIm2)::GUS constructs. When the Box IIm1 and BoxIIm2 elements were used, the GUS activity relative to the wild type BoxII element (pE:GUS) dropped significantly (FIG. 7).

In the case of the chimeric sequence pE(Box IIm2)::GUS, there waslittle, if any, GUS activity above that of non-transfected BY-2 cells(FIG. 7). These data suggest that there are endogenous transcriptionfactors in BY-2 cells that can interact with the wild type Box IIelement, which results in expression of pE:GUS in protoplasts (FIGS. 1,2 and 7). When operational derivatives of the Box II element were used,e.g., Box IIm1 and Box IIm2, the promoter activity was significantlyabolished.

Example 5

Binding Affinities of RF2a and RF2b

A previous report showed that RF2a binds to the Box II element and itsmutants with different affinities (Yin et al., 1997). To compare thebinding affinities of RF2a and RF2b with the Box II element and itsmutants, real time Surface Plasmon Resonance (“SPR”) measurements wereconducted using a BIAcore 2000 instrument. The binding affinities ofRF2a and RF2b to these DNA targets were measured on chips on whichbiotin labeled-Box II, -Box IIm1 and -Box IIm2 elements wereimmobilized.

The association and de-association constants were determined usingBIAevaluation 3.1 software—using 1:1 binding with a mass transfer model.The results are presented in FIG. 8. In general, RF2a has relativelyhigher binding affinities to the Box II, Box IIm1 and Box IIm2 elementswhen compared to RF2b. Furthermore, the DNA binding behavior of RF2a andRF2b are quite different from each other. RF2a appears to bind rapidlyto the DNA target and slowly dissociates from the target, while RF2bbinds slowly to the DNA target and releases from the target relativelyquickly. The differences in the affinity of RF2a to the Box II elementand its mutants, however, are not as dramatic as the differences ofRF2b, while the relative order of affinities to the different targetelements is the same for both proteins (FIG. 8).

To illustrate the biological relevance of the differences in the bindingaffinities described above, the pE::GUS, pE(Box IIm1)::GUS and pE(BoxIIm2)::GUS constructs were used as reporters in BY-2 protoplasttransient assays. In these assays, CaMV 35S::RF2a, CsVMV::RF2b and CaMV35S::RF2a/CsVMV::RF2b were used as effectors. All results werenormalized against the GFP internal control. The relative GUS activitiesof different sets of transfection assays are shown in FIG. 9 for the BoxIIm1 element, and FIG. 10 for the Box IIm2 element.

When the foregoing constructs were co-transfected with CaMV 35S::RF2a,the promoter activity of E(Box IIm1) and E(Box IIm2) increased 5 to 7fold (FIGS. 9 and 10). Furthermore, there was no apparent differencebetween the activation of promoters containing the Box IIm1 and Box IIm2elements. Different results were observed when the foregoing constructswere co-transfected with CsVMV::RF2b. The E(Box IIm2) promoter wasactivated about 5.8 fold by RF2b, while the E(Box IIm1) promoter wasactivated about 7 fold (FIGS. 9 and 10). Importantly, this Example showsthat the activity of the E(Box IIm1) promoter with RF2b was as high asthe expression of the E wild type promoter in BY-2 protoplasts.

The foregoing data related to the interactions between the RF2a and/orRF2b transcription factors and the target chimeric promoters suggestthat such promoters may, optionally, be designed to comprise the BoxIIm1 and/or Box IIm2 elements to create a “zero” background expressionlevel. In such case, the chimeric promoters may be activated byinitiating the expression of the RF2a and/or RF2b transcription factors,which, of course, would interact with the Box IIm1 and/or Box II2elements of the chimeric promoters, using compositions and methodsdescribed herein.

Example 6

Use of Box II and RF2a to Control Expression of Novel Chimeric Promoters

The following shows that the Box II element can be transferred tounrelated promoters, or promoter fragments, in a position dependentmanner to control heterologous gene expression. To show that the Box IIelement is portable, Box II was fused with different lengths of the CaMV35S promoter (FIG. 11). Specifically, the Box II element was fused tothe 5′ end of the chimeric promoters with a space of 7 nucleotides fromthe TATA box plus 1, 1.5, 3.0, 3.5, 5.0 and 5.5 “turns of DNA helix”(one turn=10.4 base pairs). The chimeric promoters were then insertedinto a cassette with the uidA coding sequencing and Nos terminator.

Construction of Plasmids Comprising the Box II Element and DifferentLengths of the CaMV 35S Promoter—To construct Box II and CaMV 35Schimeric promoters, the Box II element was introduced into CaMV 35Spromoter sequences of different lengths through PCR reactions using PfuDNA polymerase (Stratagen Systems, Kirkland, Wis.). Forward primers forthe PCR reactions were designed to have a HindIII restriction site,followed by the Box II sequence, which was followed by part of the5′CaMV promoter at desired positions (see FIG. 12 and Table 2 forspecific primer sequences). The GUS 3′ primer (SEQ ID NO:36) was used asreverse primer for all reactions. TABLE 2 Promoter Primer Set 5′ Primer1 −1.0hBoxII-48CaMV −1.0hBoxII-48CaMV/GUS 3′ SEQ ID NO: 37 2−1.5hBoxII-53CaMV −1.5hBoxII-53CaMV/GUS 3′ SEQ ID NO: 38 3−3.0hBoxII-69CaMV −3.0hBoxII-69CaMV/GUS 3′ SEQ ID NO: 39 4−3.5hBoxII-74CaMV −3.5hBoxII-74CaMV/GUS 3′ SEQ ID NO: 40 5−5.0hBoxII-90CaMV −5.0hBoxII-90CaMV/GUS 3′ SEQ ID NO: 41 6−5.5hBoxII-95CaMV −5.5hBoxII-95CaMV/GUS 3′ SEQ ID NO: 42

The p35S:GUS plasmid was used as template in the foregoing reactions. Inthe p35S:GUS plasmid, a NcoI restriction site was located between theCaMV 35S promoter and the GUS coding sequence. Thus, a NcoI site waspresent in all PCR products. The PCR products were restricted withHindIII/NcoI and cloned into a pE:GUS vector to replace the E promoterthrough the same set of restriction sites. The constructed plasmidscontaining the chimeric promoters labeled 1 through 6 in Table 2 werenamed p-1.0hBoxII-48CaMV:GUS, p-1.5hBoxII-53CaMV:GUS,p-3.0hBoxII-69CaMV:GUS, p-3.5hBoxII-74CaMV, p-5.0hBoxII-90CaMV:GUS, andp-5.5hBoxII-95CaMV:GUS, respectively. The controls for this set ofplasmids were generated using primer sets 1.5h-53CaMV-c (SEQ IDNO:43)/GUS3′; −3.5h-74CaMV-c (SEQ ID NO:44)/GUS3′ and −5.5h-95CaMV-c(SEQ ID NO:45)/GUS3′, which products were cloned into pE:GUS withHindIII/NcoI to replace the E promoter. The derived plasmids/constructswere named p-53CaMV:GUS, p-74CaMV:GUS and p-95CaMV:GUS, respectively.

The foregoing constructs were then transfected into non-transgenic BY-2protoplasts, and the resulting GUS activity determined. The data in FIG.13 show that when the Box II element is fused with the CaMV 35S promoterwith a space of 7 nucleotides from the TATA box plus one or more fullturns of DNA helix (p1.0hBoxII-48CaMV and p5.0hBoxII-90CaMV), geneexpression was dramatically stimulated, compared to reporter genes thatlack Box II (p-48CaMV and p-90CaMV, respectively). The p1.0hBoxII-48CaMVand p5.0hBoxII-90CaMV constructs yielded 6.9 and 4.7 fold increases inexpression level above p48CaMV and p-90CaMV, respectively, which did notcontain the Box II element.

In contrast, when the Box II element was fused to fragments of the CaMV35S promoter at positions of 7 nucleotides from the TATA box plusmultiples of 0.5 turns of DNA helix (p-1.5hBox II-53CaMV versusp-53CaMV; p-3.5hBox II-74CaMV versus p-74CaMV; and p-5.5hBox II-95CaMVversus p-95CaMV), there was much less or no stimulation of geneexpression. Of course, these results indicate that the Box II element,and its operational derivatives, can be used to control and/or enhancegene expression in unrelated promoters, preferably, when it is locatedapproximately 7 nucleotides from the TATA box plus one or more fullturns of DNA helix.

To illustrate the regulatory effect of transcription factors RF2a andRF2b on the activity of the Box II element and novel chimeric promoterscontaining the Box II element, each plasmid/construct illustrated inFIG. 11 was tested in transgenic BY-2 protoplasts that produce RF2a, orRF2a plus RF2b. In these experiments, as shown in FIG. 14, the trend ofpromoter stimulation was consistent with that shown in non-transgenicBY-2 cells, i.e., activation of promoters that contain the Box IIelement at 7 nucleotides plus 1.0 and 5.0 helices distance from the TATAbox was higher than that of the promoters in which the Box II elementwas placed 1.5, 3.5, and 5.5 helices distance from the TATA box. Thetotal amount of GUS expression exhibited by the chimeric promoterconstructs, however, was much greater in transgenic cell lines thatproduce elevated levels of RF2a (FIG. 14(A)), or RF2a plus RF2b (FIG.14(B)), than in non-transgenic protoplasts that did not contain elevatedlevels of such proteins (compare the relative GUS expression levels inFIG. 14 to FIG. 13).

The foregoing data from BY-2 wild type and transgenic cell linesindicate that the Box II element, and its operational derivatives, canregulate the expression of unrelated promoters, e.g., the CaMV 35Schimeric promoters described above, as it can in the RTBV promoter.Furthermore, the data indicate that the effect of the Box II element,and its operational derivatives, is, preferably, imparted in a positionand/or orientation dependent manner—as described above.

Example 7

Validation of Transient Assay Data From Tobacco BY-2 Protoplasts inTransgenic Arabidopsis

To evaluate the data presented above from the transient assays, binaryvectors were built and transformed into Arabidopsis plants throughAgrobacterium-mediated transformation. The set of binary vectors thatwere transformed into plants were constructs with different deletions ofthe RTBV promoter, which comprised the various portions of the Efragment described in Example 1; the E fragment containing either theBox IIm1 or Box IIm2 element; or the wild type E fragment (See FIG.15A). In the transformed Arabidopsis plants, the activity of thechimeric promoters, which comprised the Box IIm1 or Box IIm2 element,was near the basal level of expression, which was observed for theconstruct p-E(32)::GUS, in which all the cis elements of RTBV promoterup-stream of the TATA box were removed (FIG. 15B). Thus, the foregoingdata agree with the data generated in the transient protoplasts analysisdescribed in Example 5, wherein the chimeric promoters of the presentinvention may, for example, be designed to comprise the operationalderivatives Box IIm1 and/or Box IIm2 to create a near “zero” backgroundexpression level in the absence of RF2a and/or RF2b.

Example 8

RF2a Mutants with Deletions of Functional Domains

It has been shown that the bZIP protein RF2a enhances transcription invivo and in vitro. It is further known that the RF2a transcriptionfactor comprises a proline-, acidic- and glutamine-rich domain. Toanalyze the function of each domain, mutants of RF2a were created byremoving one or more of the foregoing putative domains as shown in FIG.16(A). More particularly, mutants of RF2a were created in which theproline-rich domain was removed (RF2a-ΔP); the glutamine-rich domain wasremoved (RF2a-ΔQ); the proline-rich and acidic domains were removed(RF2a-ΔPΔA); the proline- and glutamine-rich domains were removed(RF2a-ΔPΔQ); and the glutamine-rich, proline-rich and acidic domainswere removed (RF2a-3A). The coding sequence for each mutant was clonedinto the bacterial expression vector pET28a, in which a His₆ tag wasplaced at the N-terminus of the fusion protein. The derived plasmidswere named pET-RF2a (encoding full-length RF2a), pET-RF2a-ΔP,pET-RF2a-ΔQ, pET-RF2a-ΔPΔA, pET-RF2a-ΔPΔQ, and pET-RF2a-3Δ.

Plasmid Construction for Protein Purification—The sequences encoding theforegoing mutants of RF2a were created through PCR amplification. A NdeIrestriction site was added to the 5′ end of all primers, and the ATG inthe restriction site was in frame with the His₆ tag in vector pET28a(Invitrogen Corp., Carlsbad, Calif.) and served as the transcriptionstart codon for the plasmids described in Example 9. A BamHI site wasadded to all the 3′ primers with a stop codon in front of therestriction site. The primers used for amplification of the variousfragments of RF2a are listed in Table 3 below: TABLE 3 RF2a 5′ SEQ IDNO: 46 RF2a-ΔP 5′ SEQ ID NO: 47 RF2a-ΔPΔA 5′: SEQ ID NO: 48 RF2a 3′ SEQID NO: 49 RF2a-ΔQ 3′ SEQ ID NO: 50

From a complete RF2a-encoding sequence (SEQ ID NO:7), the ΔP fragmentwas amplified using primers RF2a-ΔP 5′ and RF2a 3′; ΔQ was amplifiedusing primers RF2a 5′ and RF2a-ΔQ 3′; ΔPΔA was amplified using primersRF2a-ΔPΔA 5′ and RF2a 3′; and ΔPΔQ was amplified using primers RF2a-ΔP5′ and RF2a-ΔQ 3′. The construction of pET-RF2a-3Δ and pET-RF2a weredescribed by Petruccelli et al. (2001). All of the fragments wererestricted with NdeI and BamHI and were cloned into pET28a through thesame set of restriction sites. All of the mutations were verified by DNAsequence analysis. The derived plasmids were designated pET-RF2a-ΔP,pET-RF2a-ΔQ, pET-RF2a-ΔPΔA, pET-RF2a-ΔPΔQ, pET-RF2a (encodingfull-length RF2a), and pET-RF2a-3Δ.

Protein Purification—The pET28a-derived plasmids were transformed intoEscherichia coli strain BL21 (DE3)pLysS for protein expression. Proteinexpression was induced with 0.5 mM isopropyl-β-D-thiogalactopyranosideat room temperature for 3 hours after the cell density reached A₆₀₀ of˜0.6. The His-tagged proteins were purified according to proceduresprovided by Novagen, Inc. (Madison, Wis.) under nondenaturingconditions. The purified recombinant proteins were dialyzed in 1×phosphate-buffered saline with 20% glycerol to remove imidazole andstored at −70° C.

The purified mutant proteins were then analyzed by SDS-PAGE to confirmthat each protein was its expected size (FIG. 16(B)). To confirm thateach of the mutant proteins bind to the DNA target, i.e., the Box IIelement and/or its operational derivatives, gel mobility shift assayswere carried out with the purified recombinant proteins (FIG. 16(C)).The electrophoretic mobility shift assays were carried out essentiallyas described in Yin and Beachy (1995). 100 ng of proteins purified fromthe transformed E. coli were incubated with ³²P-labeled Box IIm1 DNAprobe followed by electrophoresis in a 5% acrylamide gel (Yin et al.,1997) (FIG. 16(C)). The data presented in FIG. 16(C) demonstrate thatproteins ΔP (SEQ ID NO:68), ΔQ (SEQ ID NO:69), ΔPΔA (SEQ ID NO:70), ΔPΔQ(SEQ ID NO:71), and 3Δ (SEQ ID NO:72) of RF2a bind to the Box IIm1element.

Example 9

Contribution of RF2a Domains to Activity

The relative activity of RF2a and the RF2a mutants (described in Example8) was then measured. First, a chimeric promoter was developed with asingle copy of the Box II element fused to the 5′ end of a minimal CaMV35S promoter comprising nucleotides −48 to +8 (SEQ ID NO:66). Thechimeric promoter was ligated to the uidA coding sequence to create thereporter pBII-48Ca::GUS.

To analyze the function of the several domains of RF2a, effectors werecreated by inserting coding sequences of RF2a or the mutants of RF2a(described in Example 8) downstream of the enhanced CaMV 35S promoter inthe pMON999 vector (a gift from Monsanto Company, St. Louis, Mo.). Theresultant constructs, p35S::RF2a, p35S::RF2a-ΔP, p35S::RF2a-ΔQ,p35S::RF2a-ΔPΔA, p35S::RF2a-ΔPΔQ and p35S::RF2a-3Δ, were co-transfectedinto BY-2 protoplasts with pBII48Ca::GUS (FIG. 17(A)). Plasmid pCat-GFP,in which the GFP gene was driven by CaMV 35S promoter, was co-introducedto serve as an internal control. The following describes, in greaterdetail, the construction of these vectors and the methods employed intransfecting the same into BY-2 protoplasts.

Plasmids for protoplast transfection—The coding sequences for mutants ofRF2a were released from pET28a-derived plasmids and cloned into theplant expression vector pMON999 (a gift from Monsanto Company, St.Louis, Mo.) to place each gene downstream of an enhanced CaMV 35Spromoter, followed by a nopaline synthase terminator sequence. Theresulting effector constructs were named p35S::RF2a, p35S::RF2a-ΔP,p35S::RF2a-ΔQ, p35S::RF2a-ΔPΔA, p35S::RF2a-ΔPΔQ and p35S::RF2a-3Δ. Thereporter gene construct, pBII48Ca::GUS, was built using PCR to introducethe Box II element into a minimal CaMV 35S promoter comprisingnucleotides −48 to +8 with primers BII-48Ca 5′ (SEQ ID NO:53) (whichcontained the Box II element) and GUS 3′ (SEQ ID NO:36) using a p35S:GUSplasmid as template. The PCR product was restricted with HindIII andNcoI, and the resulting fragment was inserted into p35S::GUS to replacethe original 35S promoter.

Transfection of tobacco BY-2 protoplasts—The protoplasts were isolatedfrom tobacco cell line BY-2 as described by Watanabe et al. (1987).Approximately one million protoplasts were transfected byelectroporation with 20 μg of effector construct DNA, 15 μg of herringsperm DNA, 2.5 μg of reporter gene construct DNA, and 15 μg of pCat-GFPDNA. In samples with reporter gene alone, the total amount of DNA wasadjusted by adding 20 μg of herring sperm carrier DNA. Theelectroporation parameters used were 300 V and 250 microfarads with theBio-Rad electroporation system (Bio-Rad Laboratories, Hercules, Calif.).Protoplast samples were cultured in Murashige and Skoog medium with 0.4M mannitol, pH 5.8, at 28° C. The protoplasts were collected 24 hoursafter electroporation.

As shown in FIG. 17(B), the transactivation function of RF2a was notdecreased by removing either the proline-rich (35S::RF2a-ΔP) orglutamine-rich (35S::RF2a-ΔQ) domains or both of the domains(35S::RF2a-ΔPΔQ). In fact, the activation function of each of thesemutants was greater than that of full-length RF2a. RF2a-ΔP wassignificantly different from RF2a at the P_(0.05) level, whereas RF2a-ΔQand RF2a-ΔPΔQ were significantly different from RF2a at the P_(0.01)level (Student's t test). Also, the difference between the activity ofRF2a-ΔP and RF2a-ΔQ was significant at the P_(0.01) level, and there wasno difference between RF2a-ΔQ and RF2a-ΔPΔQ. The data suggest that theproline-rich and glutamine-rich domains do not contribute in a positiveway to the activation function of RF2a. In contrast, the activitydropped to near basal level when the acidic domain was removed(RF2a-ΔPΔA and RF2a-3Δ) (FIG. 17(B)). These results suggest that theacidic domain is responsible for the activation of gene expression byRF2a.

Example 10

Functions of RF2a Domains in Fusion Proteins

To determine whether domains of RF2a can serve as independent modules toregulate transcription, the various putative functional domains werefused with the synthetic 2C7 protein (SEQ ID NO:75), a synthetic zincfinger DNA-binding domain that specifically binds to the 2C7 DNA-bindingsite (SEQ ID NO:74), to create various “effector” constructs (FIG.18(A)). The various RF2a domains were placed either at the N-terminus orthe C-terminus of the 2C7 DNA-binding domain (“DBD”). The “reporter”construct pC7er2:GUS carried the uidA coding sequence located downstreamof a chimeric promoter comprising 6×2C7-binding sites ligated with theminimal promoter of erbB-2 (“er2”). p35S:2C7 encoded the 2C7 proteinwithout an activation domain and served as a control (FIG. 18(A)).

To create effectors with RF2a domains fused to the N-terminus of 2C7DBD, coding sequences for the acidic domain (A) (SEQ ID NO:9),proline-rich domain (P) (SEQ ID NO:54) and glutamine-rich domain (O)(SEQ ID NO:55) were amplified using primer pairs A-2C7 5′/A-2C7 3′,P-2C7 5′/P-2C7 3′, and Q-2C7 5′/Q-2C7 3′, respectively, with pET-RF2a astemplate. BglII and BamHI restriction sites were introduced into the 5′and 3′ primers, respectively. The particular sequences of the foregoingprimers are referenced in Table 4 below: TABLE 4 A-2C7 5′ SEQ ID NO: 56A-2C7 3′ SEQ ID NO: 57 P-2C7 5′ SEQ ID NO: 58 P-2C7 3′ SEQ ID NO: 59Q-2C7 5′ SEQ ID NO: 60 Q-2C7 3′ SEQ ID NO: 61

The products created by the foregoing PCR reactions were restricted withthe BglII and BamHI and cloned into pMON999 through BglII and EcoRIsites along with the DNA fragment that encoded the 2C7 DNA-bindingdomain (SEQ ID NO:76) (The 2C7 DNA-binding domain coding sequence waspreviously released from p35S:2C7 using BamHI and EcoRI). The resultingplasmids were designated p35S:A-2C7, p35S:P-2C7, and p35S:Q-2C7.

For effectors with RF2a domains at the C-terminus of the 2C7 DBD, codingsequences for the A, P, Q, and P plus A (PA) domains were released frompET-RF2a-A, pET-RF2a-P, pET-RF2a-Q, and pET-RF2a-PA using the enzymesXbaI and EcoRI and cloned into p35S:2C7-VP16 to replace the VP16 domainwith the same restriction sites. The resultant plasmids were namedp35S:2C7-A, p35S:2C7-P, p35S:2C7-Q, and p35S:2C7-PA.

Each of the foregoing effector constructs, as illustrated in FIG. 18(A),were co-transfected into BY-2 protoplasts along with the reporterconstruct. The relative GUS activities of the transfected protoplastswere subsequently determined. As shown in FIG. 18(B), when domains ofRF2a were placed at the C-terminus of the 2C7 protein, 2C7-A and 2C7-PAshowed significant activation function. When the domains were fusedindividually at the N-terminus of 2C7, the acidic domain (A-2C7)conferred stronger activation than the P(P-2C7) or Q (Q-2C7) domains.The function of the acidic domain in the fusion proteins is consistentwith its function in RF2a, although the position of this domain in thefusion proteins appears to affect its activity. The proline- andglutamine-rich domains had no effect on gene expression when they wereplaced at the C-terminus of the 2C7 DBD; however, these domains showedmild activation function when they were fused at the N-terminus of the2C7 DBD.

Example 11

Impact of Mutants of RF2a on Plant Development

Previous studies have shown that transgenic rice and tobacco plants thatoverexpressed RF2a were normal in appearance and reproduction. (Yin etal., 1997; Petruccelli et al., 2001). To determine whether mutants ofRF2a in which one or more domains were removed had a positive ornegative effect on plant development, transgenic plants that overexpressmutants of RF2a were produced. Fifteen or more independent transgenictobacco lines were developed with the constructs described below throughAgrobacterium-mediated transformation.

Plasmids for Agrobacterium-mediated transformation—The fusion genesdescribed above relating to the plant expression constructs comprisingRF2a deletion mutants were released from pMON999-derived plasmids usingNotI (blunted) and cloned into the binary vector pGA-E::GUS (Petruccelliet al., 2001) using the blunt HindIII site (downstream of a CaMV 35Spromoter sequence). The final plasmids were named pGA-E::GUS/P-35S::ΔP,pGA-E::GUS/P-35S::ΔQ, pGA-E::GUS/P-35S::ΔPΔA and pGA-E::GUS/P-35S::ΔPΔQ.A plasmid encoding full-length RF2a, p35S::RF2a, was also constructedusing the methods described herein.

Tobacco transformation—the plasmids described above were introduced intoAgrobacterium tumefaciens strain LBA4404 and used for tobaccotransformation. Leaf discs from Nicotiana tabacum cv. Xanthi NN weretransformed with the various plasmids following the protocol of Horschet al. (1988). At least 15 independent transgenic lines were producedwith each gene construct. Transgenic plants were self-fertilized, and T₁seeds were collected. The T₁ seeds were germinated on Murashige andSkoog medium (Murashige and Skoog, 1962) with kanamycin (100 mg/L)selection, and Kan^(r) seedlings were grown in a greenhouse forobservation.

Following PCR analysis, transgenic lines expressing each mutant wereobserved for phenotypic changes. T₁ generation plants with 35S::RF2a,35S::RF2a-ΔP, 35S::RF2a-ΔQ, and 35S::RF2a-ΔPΔQ did not exhibit abnormalphenotypes (FIG. 19(A)). However, 11 of 15 independent transgenic lineswith 35S::RF2a-ΔPΔA exhibited mild to severe stunting with curved leavesand substantial delay in flowering times (FIG. 19(A) & (B)).Furthermore, the internodal elongation of transgenic plants was stronglyrepressed by RF2a-ΔPΔA (FIG. 19(C), Panel 1). The phenotype caused by35S::RF2a-ΔPΔA was similar to, but less severe than, the phenotypecaused by 35S::RF2a-3A. Cross-sections of the stem of transgenic plantswith either RF2a-ΔPΔA or RF2a-3A showed that the xylem of stunted plantswas not uniformly lignified and that phloem development was altered.(FIG. 19(C)).

To confirm that the phenotype was related to transgene expression,protein extracts of the transgenic plants were analyzed via a Westernblot assay using an antibody against RF2a. Protein samples from thetransgenic leaf tissues were extracted in buffer (50 mM Na₃PO₄, pH 7.0,10 mM EDTA, 0.1% Triton X-100, 0.1% sodium lauryl sarcosine) andquantified using the DC protein assay kit (Bio-Rad Laboratories,Hercules, Calif.). 40 μg of each protein sample was separated viaSDS-PAGE and blotted onto nitrocellulose membrane. The membrane wasstained with Ponceau S (Sigma Chemical Company, St. Louis, Mo.) tomonitor protein loading prior to immuno-detection. The primary antibodyused in the immunodetection was raised in rabbits against full-lengthRF2a; the secondary antibody was horseradish peroxidase-conjugated togoat anti-rabbit antibody (Southern Biotechnology Associates, Inc.,Birmingham, Ala.). FIG. 20 shows that there is a direct correlationbetween the abnormal phenotype and the accumulation of RF2a-ΔPΔA.

Example 12

Versatility of the Gene Regulation System

As shown herein, the acidic domain of RF2a may be linked to any DNAbinding domain to regulate the expression of corresponding promoters.More specifically, the novel transcription factors of the presentinvention that comprise the acidic domain of RF2a (or substantiallysimilar sequences) and at least one DNA binding domain (“DBD”), may beused to regulate the expression of plant functional promoters thatcomprise one or more cis elements—wherein such elements are capable ofinteracting with such DNA binding domain. The interaction between suchnovel transcription factors through such DNA binding domains withcorresponding cis elements, preferably, results in the initiation, orenhancement of, transcription.

Similarly, the chimeric promoters of the present invention have beenshown to regulate transcription in the presence of RF2a and/or RF2b.More particularly, the inventors have demonstrated that the Box IIelement and/or its operational derivatives (or substantially similarsequences) may be used in connection with any plant functional promoterto regulate gene expression in the presence of RF2a, RF2b, and/or anynovel transcription factor contemplated herein which comprises an aminoacid sequence at least substantially similar to the acidic domain ofRF2a. Accordingly, it is contemplated that a plurality of differentcombinations of novel transcription factors and/or novel chimericpromoters of the present invention may be employed to regulate geneexpression.

For example, in addition to the Box II element and its operationalderivatives described herein, the RF2a and RF2b transcription factors(and related bZIP proteins) have been found to interact with certainadditional cis elements to impart regulation of transcription.Non-limiting examples of such additional cis elements are summarized inTable 5 below: TABLE 5 Common Name of cis Element DNA Sequence SEQ IDNO. rbe CCCCAAAGTCCAGCTTGAAAT SEQ ID NO:77 G3 TTAATCCAACTTGGAAAATG SEQID NO:78 AC-II CCACCACCCCC SEQ ID NO:79 4CL-1   CTTCACCACCCCACT SEQ IDNO:80 Sh1 TGGACCCTACCA SEQ ID NO:81 AHA3 AGGTCACCCCATT SEQ ID NO:82Vs-1  TGGATGTGGAAGACAGCA SEQ ID NO:83The present invention contemplates that such additional cis elements,including, without limitation, the elements referenced in Table 5, maybe used to construct novel chimeric promoters in accordance with thepresent invention. Of course, such novel chimeric promoters may be used,for example, to regulate gene expression in connection with RF2a and/orRF2b transcription factors—similar to the chimeric promoters shown anddescribed in previous Examples. It will be appreciated by those skilledin the art that chimeric promoters of the present invention, whichcomprise, for example, one or more of the additional cis elements listedin Table 5 (or substantially similar sequences), may be constructed andused in a manner similar to that described above with respect tochimeric promoters comprising Box II and/or its operational derivatives.

Still further, the present invention contemplates that the acidic domainof RF2a (SEQ ID NO:6), or substantially similar sequences, may be usedwith other DNA binding domains in the art. More particularly, thepresent invention contemplates that the acidic domain of RF2a, orsubstantially similar sequences, may be linked to any DNA binding domainfrom a plurality of classes of such domains to create noveltranscription factors capable of regulating gene expression (which wasdemonstrated in Example 10). The invention provides, for example, thatthe following classes of DNA binding domains may be used in suchcapacity: (i) basic helix-loop-helix domains (“bHLH”); (ii) DNA bindingdomains of bZIP proteins; (iii) native or synthetic zinc finger DNAbinding domains; and (iv) DNA binding domains of the E2F/DP family oftranscription factors. Non-limiting examples of such DNA binding domainsfor each class are listed in Table 6 below. Additionally, Table 6references the specific cis element with which such DNA binding domainsare known to interact (and affect gene expression). TABLE 6 Class of DBDRepresentative DBD Sequence of DBD cis Element bHLH “b/HLH/Z domain SEQID NO. 84 SEQ ID NO. 85 of USF” - from H. Sapiens bZIP “Jun” - from SEQID NO. 86 SEQ ID NO. 87 H. Sapiens Zinc-Finger “C2H2” SEQ ID NO. 88 SEQID NO. 89 E2F/DP “E2F4” SEQ ID NO. 90 SEQ ID NO. 91

Many of the DNA binding domains and cognate cis elements referenced inTable 6 are described in the literature (among others). See, forexample, Ferre-D'Amare, R. et al. (1994); Toledo-Ortiz, G. et al.(2003); Jakoby, M. et al. (2002); Segal D. J. et al. (2003); Wolfe, S.A. et al. (2001); Zheng, N. et al. (1999); and Ramirez-Parra, E. et al.(2003).

In light of the foregoing, the present invention contemplates that theDNA binding domains listed in Table 6 may be tethered to the acidicdomain of RF2a (SEQ ID NO:6), or to substantially similar sequences, tocreate novel transcription factors. The methods employed to produce suchnovel transcription factors may parallel those described above withrespect to the transcription factors comprising, for example, the 2C7domain. Those of skill in the art, however, will appreciate that anynumber of methods may be used to express such novel transcriptionfactors based on the amino acid sequences described herein.

The novel transcription factors of the present invention, whichcomprise, for example, one or more DNA binding domains referenced inTable 6 may be used to regulate the expression of appropriately designedchimeric promoters. More particularly, such transcription factors may beused to regulate the expression of chimeric promoters that comprise, forexample, the corresponding cis element referenced in Table 6 (orsubstantially similar sequences). In light of the foregoing, it shouldbe appreciated that the acidic domain of RF2a (or substantially similarsequences) may be linked to any DNA binding domain known in the art(including, without limitation, the domains listed in Table 6) toregulate the expression of corresponding promoters (which contain one ormore cis elements that may interact with such DNA binding domain toregulate transcription).

Example 13

Use of Inducible Promoters with the Gene Expression System

The gene expression system of the present invention (including thechimeric promoters, gene expression cassettes, and novel transcriptionfactors described above) may, optionally, be used in connection with aplurality of inducible promoters. In certain preferred embodiments, thepresent invention is used in connection with chemically-induciblepromoters. The following provides a non-limiting example of suchembodiments of the present invention.

Plasmid construction—The coding sequence of RF2a was released from acassette comprising the CaMV 35S promoter operably linked to aRF2a-encoding sequence, p35S::RF2a, through EcoRI/BamHI restriction. Theexcised DNA fragment was made blunt by Klenow treatment in the presenceof dNTPs. The resulting fragment was then cloned into plasmid RH3 (Rohm& Haas, Philadelphia, Pa.) to replace a luciferase coding sequence. TheRH3 plasmid originally comprised a luciferase coding sequence downstreamof a chimeric promoter that included five (5) repeats of the Gal4 DNAbinding site and the CaMV 35S minimal promoter. The chimeric promotercomprising the Gal4 DNA binding sites and the CaMV 35S minimal promoteris set forth in SEQ ID NO: 92.

The RF2a-encoding sequence, together with the chimeric promoter, werereleased from the resultant plasmid through Sal I/BamHI restrictionsites and inserted into vector pSL301, which was previously linearizedusing the same set of restriction enzymes. The chimeric promoter andRF2a-encoding sequence are referred to herein as the “5G35Sm:RF2a”sequence. The resulting plasmid is identified herein as“pSL-5G35Sm:RF2a.”

A DNA fragment containing the uidA gene operably linked to the Efragment of the RTBV promoter was released from pE:GUS through HindIII(blunted)/BamHI restriction. The excised fragment was then insertedupstream of the 5G35Sm:RF2a sequence in pSL-5G35Sm:RF2a through NdeI(blunted)/BamHI restriction sites (pSL-E:GUS/5G35Sm:RF2a). The sequencesencoding E:GUS, together with 5G35Sm:RF2a, were released frompSL-E:GUS/5G35Sm:RF2a through HindIII restriction. The excised fragmentwas then made blunt using Klenow treatment in the presence of dNTPs.

The excised GUS- and RF2a-encoding fragment was subsequently cloned intothe binary vector pCa-5GRbm:DsRed-E5/Cs:VGE, which carried the chimericreceptor gene VGE (SEQ ID NO: 93) under the control of a cassaya veinmosaic virus promoter (Cs). The resulting plasmid (pCa-EG2aV) carriedthe E:GUS, 5G35Sm:RF2a, and Cs:VGE sequences, and was used forAgrobacterium-mediated transformation of Arabidopsis thaliana.

Agrobacterium-mediated transformation—Arabidopsis transformation wasconducted using the well-known dipping method described in Clough andBent, 1998. More specifically, Agrobacterium GV3101 and pCa-EG2aV werecultured in LB medium and monitored by spectrophotometry. Once theoptical density, OD₍₆₀₀₎, of the culture reached 0.6, the culture wascollected via centrifugation. The bacterial cell pellet was re-suspendedin 5% sucrose, 0.2% Silwet 77 solution and used for inoculating theflowering Arabidopsis plants. The transformed Arabidopsis seeds werecollected at maturity and sterilized with 70% ethanol. The sterilizedseeds were germinated on MS medium containing 50 mg/L of hygromycin B toselect transgenic seedlings. The transgenic plants were grown tomaturity and seeds were collected, which are referred to as T₁ seeds.The T₁ seeds were subsequently germinated and grown to maturity.

Induction of RF2a expression—RF2a expression was induced in thetransgenic Arabidopsis plants described herein by application of a1:8000 dilution of the pesticide Intrepid® 2F (Dow AgroSciences,Indianapolis, Ind.). The active ingredient in Intrepid® 2F pesticide ismethoxyfenocide. The methoxyfenocide compound was found to enhance RF2aexpression by interaction with the expressed VGE receptor and chimericpromoter comprising Gal4 DNA binding sites described above. Accordingly,the methoxyfenocide compound served as an expression-inducing ligand,which functioned to enhance expression of the RF2a-encoding sequence.Upon application of the methoxyfenocide compound, RF2a expression wasinduced, thereby allowing RF2a to interact with the Box II-containing Efragment, which was operably linked to the uidA sequence.

Analysis of GUS activity—The relative GUS activity in the transgenicArabidopsis plants described herein was measured by histochemicalanalysis. In each of sixty-seven (67) T₁ transgenic Arabidopsis plantscarrying E:GUS, 5G35Sm:RF2a and Cs:VGE, the 1:8000 dilution of Intrepid®2F described above was applied to one true leaf, while the other leavesin each plant remained untreated. Two-days following the application ofthe expression-inducing ligand, the treated leaf together with oneuntreated leaf from the same plant were detached and subjected to GUSstaining.

More particularly, the plant leaf tissues mentioned above were submergedin stain solution containing 1 mM of X-Gluc in 100 mM sodium phosphatebuffer (pH 7.0), 2 mM K₃Fe(CN)₆, 2 mM K₄Fe(CN)₆, 0.1% Triton X-100 and20% methanol (Petruccelli et al. 2001). In order to evaluate GUSactivity, several substrates are available. The most commonly used are5-bromo-4-chloro-3-indolyl glucuronide (X-Gluc) and4-methyl-umbelliferyl-glucuronide (MUG). The reaction of GUS with X-Glucgenerates a blue color that is useful in histochemical detection of uidAgene activity. uidA activity (GUS expression) is shown in the “Treated”leaf in FIG. 21 by a grey, shaded color (compared to the predominatelywhite, “Untreated” leaf). For quantification purposes, MUG is preferred,because the umbelliferyl radical emits fluorescence under UVstimulation, thus providing better sensitivity and easy measurement byfluorometry.

Following vacuum infiltration of the previously submerged leaf tissues,the tissues were incubated at 37° C. overnight before washing with 70%(v/v) ethanol. In approximately 70% of the sixty-seven (67) plantsanalyzed, a constitutive GUS expression pattern was observed in themethoxyfenocide-treated leaves. See FIG. 21 for a subjective comparisonof GUS expression in “Treated” and “Untreated” leaf tissue.

Quantitative analysis of GUS activity in methoxyfenocide-treated plantswas then conducted. T₂ generation transgenic Arabidopsis plants fromtwelve T₁ primary lines were selected on hygromycin selection medium.The lines are individually referred to herein as EGaV-3, EGaV-5,EGaV-17, EGaV-31, EGaV-50, EGaV-51, EGaV-56, EGaV-59, EGaV-63, EGaV-70,EGaV-72, and E:GUS. For each primary line, eighteen 14-day-old T₂ plantswere used. Nine plants, in three groups, were cultured in MS hydroponicsolution containing a 1:8000 dilution of Intrepid 2F®. The remainingnine plants, in three groups, were left untreated and served ascontrols. After a three-day treatment period, the GUS activity in leaftissue samples from each plant was quantified.

Each sample of leaf tissue was ground to a powder in liquid nitrogen.Total protein was extracted from each sample by adding 300 μl ofextraction buffer. Protein concentration of each sample was quantifiedusing a Dc Protein Assay Kit (Bio-Rad Laboratories, Hercules, Calif.).GUS activity of each sample was quantified using MUG as substrate and afluorescence spectrometer (Molecular Devices, Sunnyvale, Calif.)(Petruccelli et al., 2001). Among the twelve lines, the results showedthat methoxyfenocide (Intrepid 2F®) treatment induced GUS expression byan average of 2.1 fold in relation to untreated, control plants (FIG.22A).

Western Blot analysis—To detect the expression of RF2a in selecttransgenic lines described above, either treated or untreated withIntrepid® 2F, 40 μg of protein of each sample was separated by 12%SDS-PAGE and blotted onto nitrocellulose membrane. The Arabidopsis linesanalyzed by Western Blot included EGaV50, EGaV59, EGaV63, EGaV70,EGaV72, and E:GUS. Rabbit anti-RF2a antibodies were first applied to thenitrocellulose membrane, incubated, and washed. Next, anti-rabbithorseradish peroxidase-conjugated secondary antibodies were applied tothe membrane, incubated, and washed. Finally, SuperSignal substrate(Pierce, Rockford, Ill.) was applied to the membrane, incubated, andwashed.

After the substrate was applied to the membrane, the RF2a bands wererevealed (See FIG. 22B, top panel). The presence of RF2a in the leaftissue samples that were treated with methoxyfenocide (Intrepid 2F®)correlates with the induction of GUS expression observed in similarlytreated leaf tissues (described above).

Example 14

Fragments of the Acidic Domain of RF2a

To further demonstrate the versatility of the present gene expressionsystem and, more particularly, the scope of different peptidesencompassed by the novel transcription factors of the invention,fragments of the acidic domain of RF2a were used to construct severalnovel transcription factors. More specifically, transcription factorscomprising residues 49 through 116; 49 through 96; 68 through 116; or 68through 96 of SEQ ID NO:4 (the full-length RF2a transcription factor)were constructed (35S-A-2C7 (comprising the full acidic domain of RF2a);35S-A1-2C7; 35S-A2-2C7; and 35S-A3-2C7, respectively).

The foregoing transcription factors further comprised the synthetic 2C7protein (SEQ ID NO:75)—the synthetic zinc finger DNA-binding domaindescribed above that specifically binds to the 2C7 DNA-binding site (SEQID NO:74). The various fragments of the acidic domain of RF2a were fusedto the N-terminus of the 2C7 DNA-binding domain. The gene expressioncassettes encoding such transcription factors included a CaMV 35Spromoter operatively linked to a sequence encoding the respectivefragment of the acidic domain, which was operatively linked to asequence encoding the 2C7 DNA-binding domain (SEQ ID NO:76). Thecassettes are referred to in this example collectively or individuallyas “effector construct.”

The “reporter construct,” C7er2::GUS, carried the uidA coding sequencelocated downstream of a promoter comprising 6×2C7-binding sites ligatedwith the minimal promoter of erbB-2 (“er2”) (a.k.a. the retinoblastomaminimal promoter). 35S:2C7 encoded the 2C7 protein without an activationdomain, i.e., the acidic domain of RF2a or a fragment thereof, andserved as a control.

Protoplasts isolated from suspension cultures of BY-2 cells (Nicotianatabacum L., cv. Bright Yellow-2) were transfected via electroporationusing procedures well-known in the art. More specifically, theprotoplasts were co-transfected with a mixture of DNAs, including 5 μgof reporter construct, 20 μg of a single effector construct (i.e.,35S-A-2C7, 35S-A1-2C7, 35S-A2-2C7, or 35S-A3-2C7), 5 μg of an internalcontrol plasmid comprising a CaMV 35S promoter operatively linked to aGFP-encoding sequence, and 10 μg of herring sperm DNA. Theelectroporation was conducted using a discharge of 500° F. and 250 Vthrough disposable 0.4 cm cuvettes. Each transient assay was repeatedthree times per experiment and each experiment was conducted two times.

In addition, electroporation was carried out as described above withouteffector construct (negative control); without reporter construct(negative control); or, in place of effector construct, 35S-VP16 (asequence encoding the activation domain of the herpes simplex virus)(positive control).

Quantification of GUS activity in the transfected protoplasts wascarried out 24 hours after transfection. More specifically, transfectedprotoplasts were lysed by freezing and thawing in GUS extraction buffer(pH 7.7), centrifuged, and the supernatants used for enzyme assays. GUSactivity was determined by the method of Jefferson et al. (1987). GFPactivity was determined by quantifying fluorescence using 490 nmexcitation wavelength and 530 nm emission wavelength using a standardfluorometer (Molecular Devices, Sunnyvale, Calif.).

The relative GUS activity in the BY-2 protoplasts containing reporterand effector construct, as well as the controls described above, isshown in FIG. 23. The results shown in FIG. 23 include GUS enzymeactivity compared with GFP activity and are expressed as relativefluorescent units per second. The results are the average of threeindependent transfections (with standard deviations). The results showthat the acidic domain of RF2a is a strong activator of gene expression(35S-A-2C7) and, more specifically, fragments of the acidic domaincomprising residues 49-96 of SEQ ID NO:4 (35S-A1-2C7) encompass themajority of such activity.

The many aspects and benefits of the invention are apparent from thedetailed description, and thus, it is intended for the following claimsto cover all such aspects and benefits of the invention which fallwithin the scope and spirit of the invention. In addition, becausenumerous modifications and variations will readily occur to thoseskilled in the art, the claims should not be construed to limit theinvention to the exact construction and operation illustrated anddescribed herein. Accordingly, all suitable modifications andequivalents should be understood to fall within the scope of theinvention as claimed herein.

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1. A chimeric promoter, which comprises a nucleic acid sequence selectedfrom the group consisting of SEQ ID NO:1, SEQ ID NO:2, and SEQ ID NO:3.2. The chimeric promoter of claim 1, wherein said nucleic acid sequenceis located in said chimeric promoter in a location that is approximately7 nucleotides from a TATA box plus one or more full turns of DNA helix.3. A chimeric promoter, which comprises a nucleic acid sequence selectedfrom the group consisting of (i) a sequence that is substantiallysimilar to SEQ ID NO:1; (ii) a sequence that is substantially similar toSEQ ID NO:2; and (iii) a sequence that is substantially similar to SEQID NO:3.
 4. The chimeric promoter of claim 3, wherein said nucleic acidsequence is located in said chimeric promoter in a location that isapproximately 7 nucleotides from a TATA box plus one or more full turnsof DNA helix.
 5. A gene expression cassette, which comprises: (i) achimeric promoter, wherein said promoter comprises a nucleic acidsequence that is at least substantially similar to SEQ ID NO:1; and (ii)at least one gene of interest operatively linked to said chimericpromoter.
 6. The gene expression cassette according to claim 5, whichfurther comprises a second promoter operatively linked to a secondnucleic acid sequence, wherein said second nucleic acid sequence encodesan amino acid sequence selected from the group consisting of (i) asequence that is at least substantially similar to SEQ ID NO:4 and (ii)a sequence that is at least substantially similar to SEQ ID NO:5.
 7. Thegene expression cassette according to claim 5, wherein said nucleic acidsequence that is at least substantially similar to SEQ ID NO:1 islocated in said chimeric promoter in a location that is approximately 7nucleotides from a TATA box plus one or more full turns of DNA helix. 8.The gene expression cassette according to claim 6, wherein theexpression of said second promoter is capable of beingchemically-induced.
 9. A gene expression cassette, which comprises: (i)a chimeric promoter, wherein said promoter comprises a nucleic acidsequence that is at least substantially similar to SEQ ID NO:2; and (ii)at least one gene of interest operatively linked to said chimericpromoter.
 10. The gene expression cassette according to claim 9, whichfurther comprises a second promoter operatively linked to a secondnucleic acid sequence, wherein said second nucleic acid sequence encodesan amino acid sequence selected from the group consisting of (i) asequence that is at least substantially similar to SEQ ID NO:4 and (ii)a sequence that is at least substantially similar to SEQ ID NO:5. 11.The gene expression cassette according to claim 9, wherein said nucleicacid sequence that is at least substantially similar to SEQ ID NO:2 islocated in said chimeric promoter in a location that is approximately 7nucleotides from a TATA box plus one or more full turns of DNA helix.12. The gene expression cassette according to claim 10, wherein theexpression of said second promoter is capable of beingchemically-induced.
 13. A gene expression cassette, which comprises: (i)a chimeric promoter, wherein said promoter comprises a nucleic acidsequence that is at least substantially similar to SEQ ID NO:3; and (ii)at least one gene of interest operatively linked to said chimericpromoter.
 14. The gene expression cassette according to claim 13, whichfurther comprises a second promoter operatively linked to a secondnucleic acid sequence, wherein said second nucleic acid sequence encodesan amino acid sequence selected from the group consisting of (i) asequence that is at least substantially similar to SEQ ID NO:4 and (ii)a sequence that is at least substantially similar to SEQ ID NO:5. 15.The gene expression cassette according to claim 13, wherein said nucleicacid sequence that is at least substantially similar to SEQ ID NO:3 islocated in said chimeric promoter in a location that is approximately 7nucleotides from a TATA box plus one or more full turns of DNA helix.16. The gene expression cassette according to claim 14, wherein theexpression of said second promoter is capable of beingchemically-induced.
 17. A gene expression cassette comprising: (i) afirst promoter, which comprises a nucleic acid sequence that is capableof interacting with at least one DNA Binding Domain of at least onepolypeptide, operatively linked to a gene of interest; and (ii) a secondpromoter operatively linked to a second nucleic acid sequence thatencodes a polypeptide comprising (a) an amino acid sequence that is atleast substantially similar to SEQ ID NO:6 and (b) said DNA BindingDomain capable of interacting with the nucleic acid sequence of saidfirst promoter, wherein said DNA Binding Domain is not derived from RF2aor RF2b.
 18. The gene expression cassette according to claim 17, whereinthe expression of said second promoter is capable of beingchemically-induced.
 19. A method of regulating the expression level ofat least one gene of interest, which comprises the steps of: (i)constructing the gene expression cassette of claim 5 and (ii)transforming a plant cell with said gene expression cassette.
 20. Amethod of regulating the expression level of at least one gene ofinterest, which comprises the steps of: (i) constructing the geneexpression cassette of claim 9 and (ii) transforming a plant cell withsaid gene expression cassette.
 21. A method of regulating the expressionlevel of at least one gene of interest, which comprises the steps of:(i) constructing the gene expression cassette of claim 13 and (ii)transforming a plant cell with said gene expression cassette.
 22. Amethod of regulating the expression level of at least one gene ofinterest, which comprises the steps of: (i) constructing the geneexpression cassette of claim 17 and (ii) transforming a plant cell withsaid gene expression cassette.
 23. A method of regulating the expressionlevel of at least one gene of interest, which comprises the steps of:(i) transforming a plant cell with the gene expression cassette of claim8; (ii) regenerating said plant cell into a plant; and (iii) applying tosaid plant an activating amount of a chemical inducer, wherebyapplication of said inducer causes expression of the nucleic acidsequence to which said second promoter is operatively linked.
 24. Amethod of regulating the expression level of at least one gene ofinterest, which comprises the steps of: (i) transforming a plant cellwith the gene expression cassette of claim 12; (ii) regenerating saidplant cell into a plant; and (iii) applying to said plant an activatingamount of a chemical inducer, whereby application of said inducer causesexpression of the nucleic acid sequence to which said second promoter isoperatively linked.
 25. A method of regulating the expression level ofat least one gene of interest, which comprises the steps of: (i)transforming a plant cell with the gene expression cassette of claim 16;(ii) regenerating said plant cell into a plant; and (iii) applying tosaid plant an activating amount of a chemical inducer, wherebyapplication of said inducer causes expression of the nucleic acidsequence to which said second promoter is operatively linked.
 26. Amethod of regulating the expression level of at least one gene ofinterest, which comprises the steps of: (i) transforming a plant cellwith the gene expression cassette of claim 18; (ii) regenerating saidplant cell into a plant; and (iii) applying to said plant an activatingamount of a chemical inducer, whereby application of said inducer causesexpression of the nucleic acid sequence to which said second promoter isoperatively linked.
 27. A plant cell which has been transformed with thegene expression cassette of claim
 5. 28. A plant cell which has beentransformed with the gene expression cassette of claim
 9. 29. A plantcell which has been transformed with the gene expression cassette ofclaim
 13. 30. A plant cell which has been transformed with the geneexpression cassette of claim
 17. 31. A transcription factor capable ofregulating the expression level of at least one gene of interest, whichconsists essentially of an amino acid sequence that is at leastsubstantially similar to SEQ ID NO:6.
 32. A nucleic acid sequence, whichencodes the transcription factor of claim
 31. 33. A plant cell which hasbeen transformed with the nucleic acid sequence of claim
 32. 34. Atranscription factor capable of regulating the expression level of atleast one gene of interest, which comprises an amino acid sequence thatis at least substantially similar to SEQ ID NO:6 and any other aminoacid sequence not derived from RF2a or RF2b.
 35. A nucleic acidsequence, which encodes the transcription factor of claim
 34. 36. Aplant cell which has been transformed with the nucleic acid sequence ofclaim
 35. 37. A transcription factor capable of regulating theexpression level of at least one gene of interest, which comprises afragment of the acidic domain of RF2a.
 38. A nucleic acid sequence,which encodes the transcription factor of claim
 37. 39. A plant cellwhich has been transformed with the nucleic acid sequence of claim 38.